1 |
ACEScanhttp://genes.mit.edu/acescan/ |
| Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB. Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A. 2005;102(8):2850-2855. doi:10.1073/pnas.0409742102
| 2005 | |
algorithm designed to detect alternative splicing events from RNA sequencing (RNA-Seq) data Gives graphical representation of all ACEScan scored exons. |
2 |
AceViewhttp://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html |
| Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 2006;7 Suppl 1(Suppl 1):S12.1-S12.14. doi:10.1186/gb-2006-7-s1-s12
| 2006 | |
provides a strictly cDNA-supported view of the human transcriptome and the genes by summarizing all quality-filtered human cDNA data from GenBank, dbEST and the RefSeq Compact Gene diagram is shown as an output, which marks the exon length. Number of cDNA's supporting each intron, good proteins, partial or not good proteins are also marked. |
3 |
AgenDA - Alignment based Gene Detection Algorithmhttp://bibiserv.techfak.uni-bielefeld.de/agenda/ |
| Taher L, Rinner O, Garg S, et al. AGenDA: homology-based gene prediction. Bioinformatics. 2003;19(12):1575-1577. doi:10.1093/bioinformatics/btg181
| 2003 | |
homology-based gene-finding program and, searches for conserved splicing signals and start/stop codons around regions of local sequence similarity 1) Results are obtained in e-mail 2) Gene information provides Gene number. 3) Provides information about the reading frame (0,1,2) 4) Gives information about the DNA strand, whether + or - |
4 |
Agenehttp://servers.binf.ku.dk/agene/ |
| Munch K, Krogh A. Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics. 2006;7:263. Published 2006 May 21. doi:10.1186/1471-2105-7-263
| 2006 | |
generates a species-specific gene predictor from a set of reliable mRNA sequences and a genome. "1) Requires registration. 2) Returns error ""Please note that this software is no longer being supported or updated."" as on 26th july 2012 3) GeneMachine is available by anonymous FTP at ftp://ftp.nhgri.nih.gov/pub/software/genemachine/." |
5 |
Alexa-Seq - Alternative Expression Analysis By RNA Sequencinghttp://www.alexaplatform.org/alexa_seq/index.htm |
| Griffith M, Griffith OL, Mwenifumbo J, et al. Alternative expression analysis by RNA sequencing. Nat Methods. 2010;7(10):843-847. doi:10.1038/nmeth.1503
| 2010 | |
analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. 1) ALEXA-Seq annotation databases for eight species, raw data, source code, etc. can be downloaded. 2) Gene information includes chromosome number, start, end, strand, size and type of gene. |
6 |
ApiESTDBhttp://www.cbil.upenn.edu/paradbs-servlet/ |
| Li L, Crabtree J, Fischer S, et al. ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. Nucleic Acids Res. 2004;32(Database issue):D326-D328. doi:10.1093/nar/gkh112
| 2004 | |
provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. URL not working as on 14 Dec 2012 |
7 |
ASDB - Alternative Splicing Databasehttp://cbcg.nersc.gov/asdb |
| Gelfand MS, Dubchak I, Dralyuk I, Zorn M. ASDB: database of alternatively spliced genes. Nucleic Acids Res. 1999;27(1):301-302. doi:10.1093/nar/27.1.301
| 1999 | |
incorporates information about alternatively spliced genes, their products and expression patterns. URL not working as on 14 Dec 2012 |
8 |
ASPic - Alternative Splicing Predictionhttp://t.caspur.it/ASPIC/index.php |
| Bonizzoni P, Rizzi R, Pesole G. ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics. 2005;6:244. Published 2005 Oct 5. doi:10.1186/1471-2105-6-244
| 2005 | |
provides the minimal set of non-mergeable transcript isoforms compatible with the detected splicing events. 1) Requires registration. 2) Gene name Brca1 and mybl2 as well as uploaded sequence didn't receive any results when used in the option of 'RUN Aspic'. 3) Provides option of retrieving Unigene ID for input. 4) Results are obtained in E-mail. 5) Gives genomic and transcript sequences. 6) Gene structure view is provided, showing Refseq exon, Novel exon, Refseq Intron, Novel intron, Fuzzy Intron, Canonical splice site and Non-Canonical splice site. 7) Shows 3'UTR and 5'UTR, Poly A site 8) Splice si |
9 |
ASRG - ArabidopsisSplicing Related Geneshttp://www.plantgdb.org/prj/SiP/SRGD/ASRG |
| Wang BB, Brendel V. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol. 2004;5(12):R102. doi:10.1186/gb-2004-5-12-r102
| 2004 | |
contain information on gene structure, alternative splicing, gene duplications and phylogenetic relationships 1) Didn't return any results using search fields when tried multiple times. 2) Browsing results not displayed properly due to some error in page. |
10 |
ASTRA - Alternative Splicing and TRanscription Archiveshttp://alterna.cbrc.jp/ |
| Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O. Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics. 2006;22(10):1211-1216. doi:10.1093/bioinformatics/btl067
| 2006 | |
a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand 1) Gene information includes Gene name, chromosome number, strand, position and number of patterns. 2) Sequence of gene can be downloaded. 3) Data of Alternative Splicing can also be downloaded. |
11 |
Augustushttp://augustus.gobics.de/submission |
| Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34(Web Server issue):W435-W439. doi:10.1093/nar/gkl200
| 2006 | |
tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure 1) This method allows approximation of the true intron length distribution more accurately than do existing programs. 2) It gives alignment results.These can be downloaded as well. 3) Gives predicted coding sequences. |
12 |
BDGP - Berkeley Drosophila Genome Projecthttp://www.fruitfly.org/seq_tools/splice.html |
| Spradling AC, Stern D, Beaton A, et al. The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics. 1999;153(1):135-177. doi:10.1093/genetics/153.1.135
| 1999 | |
generates single P-element insertion strains that each mutate unique genomic open reading frames 1) Splice Site details include start position, end position and score for acceptor as well as donor sites. 2) The exon/Intron boundary is shown by enlarging the font size. |
13 |
BGF - Beijing Gene Finderhttp://tlife.fudan.edu.cn/bgf/ |
| Jin J. Identification of protein coding regions of rice genes using alternative spectral rotation measure and linear discriminant analysis. Genomics Proteomics Bioinformatics. 2004;2(3):167-173. doi:10.1016/s1672-0229(04)02022-4
| 2004 | |
use both coding information and splicing signals, perform better than those using only splicing signals |
14 |
BLAT - BLAST like Alignment toolhttp://genome.ucsc.edu/cgi-bin/hgBlat?command=start |
| Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002;12(4):656-664. doi:10.1101/gr.229202
| 2002 | |
delivers a list of exons sorted by exon size, with alignments extending slightly beyond the edge of each exon 1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour. |
15 |
C-Ithttp://C-It.mpi-bn.mpg.de |
| Gellert P, Jenniches K, Braun T, Uchida S. C-It: a knowledge database for tissue-enriched genes. Bioinformatics. 2010;26(18):2328-2333. doi:10.1093/bioinformatics/btq417
| 2010 | |
provide more comprehensive coverage of gene expression patterns and tissue-enriched splicing isoforms. 1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried gene |
16 |
ChickGCE - Chicken Germ Cell ESThttp://chickGCE.snu.ac.kr |
| Kim H, Lim D, Han BK, et al. ChickGCE: a novel germ cell EST database for studying the early developmental stage in chickens. Genomics. 2006;88(2):252-257. doi:10.1016/j.ygeno.2006.03.015
| 2006 | |
provides functional annotation, identification, and putative embryonic germ-cell-specific novel transcripts based on the Gene Ontology database, as well as statistical analyses of expression patterns and pair-wise comparisons of two types of tissue- and germ-cell-specific alternative splicing events in the chicken. URL not working as on 14 Dec 2012 |
17 |
ChimerDBhttp://genome.ewha.ac.kr/ChimerDB/ |
| Kim N, Kim P, Nam S, Shin S, Lee S. ChimerDB--a knowledgebase for fusion sequences. Nucleic Acids Res. 2006;34(Database issue):D21-D24. doi:10.1093/nar/gkj019
| 2006 | |
database of fusion sequences encompassing bioinformatics analysis of mRNA and expressed sequence tag (EST) sequences in the GenBank, manual collection of literature data and integration with other known database such as OMIM. Url working, but gives error in result page as on 27th July 2012 |
18 |
CONTRAST - CONditionally TRAined Search for Transcriptshttp://contra.stanford.edu/contrast/ |
| Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 2007;8(12):R269. doi:10.1186/gb-2007-8-12-r269
| 2007 | |
CONTRAST predicts exact coding region structures Predicitions downloadable or can be browsed by using UCSC genome browser. |
19 |
CRYP-SKIP serverhttp://cryp-skip.img.cas.cz/ |
| Divina P, Kvitkovicova A, Buratti E, Vorechovsky I. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet. 2009;17(6):759-765. doi:10.1038/ejhg.2008.257
| 2009 | |
distinguishes the two aberrant splicing outcomes from DNA sequences. The server gives exonic sequence with intronic flanks as the output. The sequence contains predicted cryptic 5' splice sites (red marks) and 3' splice sites (blue marks) |
20 |
DisProt - Database Of Protein Disorderhttp://www.disprot.org/protein.php?ID=DP00009 |
| Vucetic S, Obradovic Z, Vacic V, et al. DisProt: a database of protein disorder. Bioinformatics. 2005;21(1):137-140. doi:10.1093/bioinformatics/bth476
| 2005 | |
provides structure and function information about proteins that lack a fixed three-dimensional (3D) structure under putatively native conditions |
21 |
ESEfinderhttp://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home |
| Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res. 2003;31(13):3568-3571. doi:10.1093/nar/gkg616
| 2003 | |
facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. 1) Results can be obtained by E-mail. 2) The position, site and score are given in the tabular format.3) The graphical results are also displayed. |
22 |
EuGene'Homhttp://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl |
| Foissac S, Bardou P, Moisan A, Cros MJ, Schiex T. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res. 2003;31(13):3742-3745. doi:10.1093/nar/gkg586
| 2003 | |
gene prediction software for eukaryotic organisms based on comparative analysis. 1)Gene information comprises of the number, strand, phase and Frame information. 2) The graphical output shows a)6 possible coding phases (+1, +2, +3 for the direct strand, -1, -2, -3 for the reverse one) b) introns on the forward (IF) and reverse (IR) strands c) other non coding regions (IG for intergenic or UTR regions) 3) Start, stop, donor and acceptor sites are marked on the graph. 4) The program is more specifically tuned for angiosperms. |
23 |
EX-SKIPhttp://ex-skip.img.cas.cz/ |
| Raponi M, Kralovicova J, Copson E, et al. Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6. Hum Mutat. 2011;32(4):436-444. doi:10.1002/humu.21458
| 2011 | |
predict a splicing change in the majority of the mutations 1) Compares the ESE/ESS profile of a wild-type and a mutated allele to quickly determine, which exonic variant has the highest chance to skip this exon. 2) It calculates the total number of ESSs, ESEs and their ratio. 3) It computes the number of RESCUE-ESEs, FAS-ESSs, PESEs/PESSs, neighborhood inference and EIE/IIEs for each segment. |
24 |
Exon minerhttp://ae.hgc.jp/exonminer/otp.php |
| Numata K, Yoshida R, Nagasaki M, Saito A, Imoto S, Miyano S. ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinformatics. 2008;9:494. Published 2008 Nov 26. doi:10.1186/1471-2105-9-494
| 2008 | |
well suited for analysis of exon array data "Returns message ""ExonMiner is currently in maintenance. Sorry for the inconvenience.""" |
25 |
| Pareja E, Pareja-Tobes P, Manrique M, Pareja-Tobes E, Bonal J, Tobes R. ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms. BMC Microbiol. 2006;6:29. Published 2006 Mar 15. doi:10.1186/1471-2180-6-29
| 2006 | |
database for exploring Extragenic regions and Transcriptional information in bacteria and archaea. |
26 |
fast DB - Friendly Alternative Splicing and Transcription Databasehttp://www.fast-db.com/ |
| de la Grange P, Dutertre M, Martin N, Auboeuf D. FAST DB: a website resource for the study of the expression regulation of human gene products. Nucleic Acids Res. 2005;33(13):4276-4284. Published 2005 Jul 28. doi:10.1093/nar/gki738
| 2005 | |
defines easily and accurately the exon content of all known transcripts produced by human genes. Gene information includes description about the Gene, chromosome number, strand information. |
27 |
FESD - Functional Element SNP's Databasehttp://combio.kribb.re.kr/ksnp/resd/. |
| Kang HJ, Choi KO, Kim BD, Kim S, Kim YJ. FESD: a Functional Element SNPs Database in human [published correction appears in Nucleic Acids Res. 2005;33(1):449]. Nucleic Acids Res. 2005;33(Database issue):D518-D522. doi:10.1093/nar/gki082
| 2005 | |
categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. URL not working as on 30th july 2012 |
28 |
FirstEF - First Exon Finderhttp://rulai.cshl.edu/tools/FirstEF/ |
| Davuluri RV. Application of FirstEF to find promoters and first exons in the human genome. Curr Protoc Bioinformatics. 2003;Chapter 4:Unit4.7. doi:10.1002/0471250953.bi0407s01
| 2003 | |
a method for predicting the first exons and promoters. 1) Gives predictions on direct as well as complementary strand. 2) Gives serial number of predicted exon cluster. 3) Gives predicted Promoter of length 570 bp. 4) Gives a posteriori probability of promoter for a given window of 570 bp. 5) Gives posteriori probablity of exon for a given GT and promoter region. 6) Gives posteriori probability of donor for a given GT. 7)Gives Boundaries of CpG window of length 201. 8) Gives rank of first exon within a cluster. 9) Results can be obtained by e-mail. |
29 |
FUGOID - Functional Genomics Of Organellar Intron Databasehttp://wnt.cc.utexas.edu/~ifmr530/introndata/main.htm. |
| Li F, Herrin DL. FUGOID: functional genomics of organellar introns database. Nucleic Acids Res. 2002;30(1):385-386. doi:10.1093/nar/30.1.385
| 2002 | |
collects and integrates various functional and structural data on organellar (mitochondrial and chloroplast) introns. URL not working as on 14 Dec 2012 |
30 |
GAPP - Genome Annotating Proteomic Pipelinehttp://www.gapp.info/index.php |
| Shadforth I, Xu W, Crowther D, Bessant C. GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. J Proteome Res. 2006;5(10):2849-2852. doi:10.1021/pr060205s
| 2006 | |
capable of finding any peptides expected, including those that cross intron-exon boundaries, and those due to single nucleotide polymorphisms (SNPs), alternate splicing, and post-translational modifications (PTMs). "1) Requires registration. 2) Returns message ""The registration is currently disabled for maintainance purpose. Sorry about any inconvenience it may cause."" when clicked for registration. 3) Search option using ""Mine the GAPP."" " |
31 |
GatExplorer - Genomic and Transcriptomic Explorerhttp://bioinfow.dep.usal.es/xgate/principal.php |
| Risueño A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics. 2010;11:221. Published 2010 Apr 29. doi:10.1186/1471-2105-11-221
| 2010 | |
allows visualization of probes in their genomic context together with any associated protein-coding or noncoding transcripts. Gene information includes chromosome location and gene description. |
32 |
GeneBuilderhttp://zeus2.itb.cnr.it/~webgene/genebuilder.html |
| Milanesi L, D'Angelo D, Rogozin IB. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 1999;15(7-8):612-621. doi:10.1093/bioinformatics/15.7.612
| 1999 | |
prediction of functional signals and coding regions by different approaches in combination with similarity searches in proteins and EST databases. Gene model and Coding potential are shown graphically, but are not loading as on 25th july 2012 |
33 |
GeneCardshttp://www.genecards.org/ |
| Safran M, Dalah I, Alexander J, et al. GeneCards Version 3: the human gene integrator. Database (Oxford). 2010;2010:baq020. Published 2010 Aug 5. doi:10.1093/database/baq020
| 2010 | |
visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways Disorders/ Disease information is also provided.One can know the Function, Genomic View, Orthologs and paralogs for a particular gene. Along with this, Pathway information, domain and family information is displayed |
34 |
GeneMarkhttp://exon.biology.gatech.edu/eukhmm.cgi#prot |
| Borodovsky M, Lomsadze A, Ivanov N, Mills R. Eukaryotic gene prediction using GeneMark.hmm. Curr Protoc Bioinformatics. 2003;Chapter 4:Unit4.6. doi:10.1002/0471250953.bi0406s01
| 2003 | |
method for detecting genes in eukaryotic DNA sequences. 1) Results can be obtained by e-mail. 2) Gene information includes the Gene number and strand type. 3) Frame information is also given. |
35 |
GeneNesthttp://genenest.molgen.mpg.de/ |
| Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M. GeneNest: automated generation and visualization of gene indices. Trends Genet. 2000;16(11):521-523. doi:10.1016/s0168-9525(00)02116-8
| 2000 | |
designed to facilitate the study of alternative splicing by providing comprehensive annotations and data related to splice variants. |
36 |
GeneSeqerhttp://deepc2.psi.iastate.edu/cgi-bin/gs.cgi |
| Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics. 2004;20(7):1157-1169. doi:10.1093/bioinformatics/bth058
| 2004 | |
capable of aligning thousands of ESTs with a long genomic sequence in a reasonable amount of time 1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences. |
37 |
Geniehttp://www.fruitfly.org/seq_tools/genie.html |
| Reese MG, Eeckman FH, Kulp D, Haussler D. Improved splice site detection in Genie. J Comput Biol. 1997;4(3):311-323. doi:10.1089/cmb.1997.4.311
| 1997 | |
Gene Finder Based on Generalized HIDden Markov Models. Improved splice site predictor for the genefinding program |
38 |
GenomeScanhttp://genes.mit.edu/genomescan.html |
| Yeh RF, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome. Genome Res. 2001;11(5):803-816. doi:10.1101/gr.175701
| 2001 | |
can accurately identify the exon-intron structures of genes in finished or draft human genome sequence with a low rate of false-positives. No output result obtained. PS file not supported on server and PDF file shown blank |
39 |
GenomeThreaderhttp://www.plantgdb.org/cgi-bin/GenomeThreader/gth.cgi |
| Gremme, G. (2014). GenomeThreader Gene Prediction Software.
| 2014 | |
designed for the precise alignment of cDNA or EST sequences to genomic DNA, which facilitates the identification and analysis of alternative splicing events |
40 |
GENSCANhttp://genes.mit.edu/GENSCAN.html |
| Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997;268(1):78-94. doi:10.1006/jmbi.1997.0951
| 1997 | |
identifies complete exon/intron structures of genes in genomic DNA 1) One can request for a local copy of program to process large number of sequences. 2) Also gives frame and phase information of exon. |
41 |
GenView 2http://zeus2.itb.cnr.it/~webgene/wwwgene.html |
| Ronneberg TA, Freeland SJ, Landweber LF. Genview and Gencode : a pair of programs to test theories of genetic code evolution. Bioinformatics. 2001;17(3):280-281. doi:10.1093/bioinformatics/17.3.280
| 2001 | |
tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. 1) Results can be mailed to the user as per his/her choice. 2) The result page is not returning any results except the sequence and the translated peptide sequence that has been submitted as on25-july-2012 |
42 |
GLIMMER - Gene locator and Interpolated Markov Model ERhttp://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi |
| Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999;27(23):4636-4641. doi:10.1093/nar/27.23.4636
| 1999 | |
designed for identifying genes in prokaryotic and eukaryotic genomes using a machine learning approach based on Interpolated Markov Models (IMMs) Gives information about ORF, start, end, frame and score. |
43 |
GOOD - Gene Oriented Ortholog Databsehttp://goods.ibms.sinica.edu.tw/goods/index.html |
| Ho MR, Chen CH, Lin WC. Gene-oriented ortholog database: a functional comparison platform for orthologous loci. Database (Oxford). 2010;2010:baq002. doi:10.1093/database/baq002
| 2010 | |
employs genomic locations of transcripts to cluster AS-derived isoforms prior to ortholog delineation to eliminate the interference from AS 1) Gives chromosome number and strand information as gene information. 2) Only the number of transcripts are given,which are linked to homologene (ncbi). 3) Also annotations from gene ontology are mentioned (molecular function, biological process, cellular component). 4) Reference transcripts, processed transcription units, orthologous tables, gene ontology can be downloaded. 5) Gives the detail of the different trans |
44 |
GRL - Gene Resource Locatorhttp://grl.gi.k.u-tokyo.ac.jp |
| Honkura T, Ogasawara J, Yamada T, Morishita S. The Gene Resource Locator: gene locus maps for transcriptome analysis. Nucleic Acids Res. 2002;30(1):221-225. doi:10.1093/nar/30.1.221
| 2002 | |
assembles gene maps that include information on gene-expression patterns, cis-elements in regulatory regions and alternatively spliced transcripts URL not working as on 14 Dec 2012 |
45 |
HMMGenehttp://www.cbs.dtu.dk/services/HMMgene/ |
| Krogh A. Using database matches with for HMMGene for automated gene detection in Drosophila. Genome Res. 2000;10(4):523-528. doi:10.1101/gr.10.4.523
| 2000 | |
gene prediction tool that utilizes Hidden Markov Models (HMMs) to identify gene structures in genomic sequences 1) Score (0 or 1), strand and Frame information is also given. 2) Predicted donor and acceptor site with position of base before and after splice site is given. |
46 |
HOT-SKIPhttp://hot-skip.img.cas.cz/ |
| Grodecká L, Buratti E, Freiberger T. Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics?. Int J Mol Sci. 2017;18(8):1668. Published 2017 Jul 31. doi:10.3390/ijms18081668
| 2017 | |
tool designed specifically to identify and analyze exon skipping events, which are a common type of alternative splicing 1) Lists predicted splicing regulatory sequences for all possible point mutations at each exon position. 2) It considers all possible exonic substitutions, except for changes in the first and the last three positions of the exon, ie. splice site consensus signals. |
47 |
HS3D - Homo sapiens Splice Site Datasethttp://www.sci.unisannio.it/docenti/rampone/ |
| Pasquale Pollastro and Salvatore Rampone. HS3D, a dataset of Homo sapiens splice regions, and its extraction procedure from a major public database. Int. J. Mod. Phys. C 13, 1105 (2002).
| 2002 | |
dataset specifically designed to aid in the study and prediction of splice sites in the human genome. 1) Result is only downloadable. No search option is provided. 2) Intron-Exon true splice sites extracted from filtered Genbank and Intron- exon false splice sites extracted from genbank are downloadable in Zip format. |
48 |
HSF - Human Splicing Finderhttp://www.umd.be/HSF/ |
| Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37(9):e67. doi:10.1093/nar/gkp215
| 2009 | |
predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence 1) A tool is provided to mutate a given sequence. 2) Potential splice sites, Potential branch points and Splicing motifs are shown in graphical format. 3) The information about sequence position, cDNA position, Splice site type, Motif sequence, New potential splice site and consensus value is provided in a tabular format. 4) Enhancer motifs along with sequence position are provided in tabular format. 5) Some of the calculations of ESE motifs are performed using new matrices, which are experiment |
49 |
IGMS - Intergrated Genetic Map Servicehttp://www.bioinf.mdc-berlin.de/igms/ |
| Pospisil H, Herrmann A, Pankow H, Reich JG. A database on alternative splice forms on the integrated genetic map service (IGMS). In Silico Biol. 2003;3(1-2):229-234.
| 2003 | |
comprehensive information system that combines the knowledge from genomic sequence, genetic map and genetic disorders databases URL not working as on 14 Dec 2012 |
50 |
Introneratorhttp://hgwdev-hiram.cse.ucsc.edu/IntronWS120/index.html |
| Kent WJ, Zahler AM. The intronerator: exploring introns and alternative splicing in Caenorhabditis elegans. Nucleic Acids Res. 2000;28(1):91-93. doi:10.1093/nar/28.1.91
| 2000 | |
set of web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans Displays Splicing diagrams. |
51 |
MatDB - MIPS Arabidopsis thaliana Databasehttp://mips.gsf.de/proj/thal/db. |
| Schoof H, Ernst R, Nazarov V, Pfeifer L, Mewes HW, Mayer KF. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res. 2004;32(Database issue):D373-D376. doi:10.1093/nar/gkh068
| 2004 | |
provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. URL not working as on 14 Dec 2012 |
52 |
MGAlignIthttp://proline.bic.nus.edu.sg/mgalign/mgalignit.html |
| Lee BT, Tan TW, Ranganathan S. MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences. Nucleic Acids Res. 2003;31(13):3533-3536. doi:10.1093/nar/gkg561
| 2006 | |
novel, rapid, memory efficient and practical method for aligning mRNA/EST and genome sequences. |
53 |
MZEF - Michael Zhang's Exon Finderhttp://rulai.cshl.edu/tools/genefinder/ |
| Zhang MQ. Using MZEF to find internal coding exons. Curr Protoc Bioinformatics. 2002;Chapter 4:. doi:10.1002/0471250953.bi0402s00
| 2002 | |
designed to help identify one of the most important classes of exons, i.e. the internal coding exons, in human genomic DNA sequences. 1) Gives the posterior probability. 2) Gives Frame preference score for ith frame. 3) Gives acceptor and donor score in splice site details. 4) Gives coding preference score. 5) Results can be obtained in E-mail. |
54 |
NCBI ORF Finder (Open Reading Frame Finder)http://www.ncbi.nlm.nih.gov/gorf/gorf.html |
| Rombel IT, Sykes KF, Rayner S, Johnston SA. ORF-FINDER: a vector for high-throughput gene identification. Gene. 2002;282(1-2):33-41. doi:10.1016/s0378-1119(01)00819-8
| 2002 | |
for selecting open reading frames (ORFs) from randomly fragmented genomic DNA fragments. |
55 |
NetPlantGene Serverhttp://www.cbs.dtu.dk/services/NetPGene/ |
| Justesen AF, Jespersen HM, Welinder KG. Analysis of two incompletely spliced Arabidopsis cDNAs encoding novel types of peroxidase. Biochim Biophys Acta. 1998;1443(1-2):149-154. doi:10.1016/s0167-4781(98)00205-x
| 1998 | |
Server for splice-site prediction 1. No option for uploading the file. 2) Sequence must be more than 200 bp long and less than 80,000 bp. 3) Also give detail about the number of nucleotides and G+C content. 4) Lists predictions for donor and acceptor splice sites. 5) Gives branch point predictions. 6) Gives the predicted frame offset (1,2 or 3) of acceptor/ donor site. 7) The sequence strand, whether its direct or complementary. 8) Gives 20 bases of sequence around the predicted site. |
56 |
OMA 2011 - Orthologous Matrix 2011http://omabrowser.org/cgi-bin/gateway.pl |
| Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res. 2011;39(Database issue):D289-D294. doi:10.1093/nar/gkq1238
| 2011 | |
database that identifies orthologs among publicly available, complete genomes. "Returns error ""Service Temporarily Unavailable"" as on 30th july 2012" |
57 |
ORF Finderhttp://www.bioinformatics.org/sms/orf_find.html |
| Rombel IT, Sykes KF, Rayner S, Johnston SA. ORF-FINDER: a vector for high-throughput gene identification. Gene. 2002;282(1-2):33-41. doi:10.1016/s0378-1119(01)00819-8
| 2002 | |
for selecting open reading frames (ORFs) from randomly fragmented genomic DNA fragments. |
58 |
PESX - Putative Exonic Splicing Enhancers/Silencershttp://cubweb.biology.columbia.edu/pesx/ |
| Xiao J, Uitti RJ, Zhao Y, et al. Mutations in CIZ1 cause adult onset primary cervical dystonia. Ann Neurol. 2012;71(4):458-469. doi:10.1002/ana.23547
| 2012 | |
identify and analyze exonic splicing enhancers (ESEs) and exonic splicing silencers (ESSs). The junction details include the Putative Exonic Splicing Enhancers and Silencers, Marked in red and green color respectively. |
59 |
Plant MPSS - Plant Massively Parallel Signature Sequencinghttp://mpss.udel.edu |
| Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC. Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res. 2006;34(Database issue):D731-D735. doi:10.1093/nar/gkj077
| 2006 | |
measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts |
60 |
PolyA_DB 2http://polya.umdnj.edu/PolyA_DB2 |
| Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 2007;35(Database issue):D165-D168. doi:10.1093/nar/gkl870
| 2007 | |
provides information on polyadenylation sites in eukaryotic mRNAs URL not working as on 14 Dec 2012 |
61 |
RARGE - RIKEN ArabidopsisGenome Encyclopediahttp://rarge.psc.riken.jp/a_splicing/ |
| Sakurai T, Satou M, Akiyama K, et al. RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic Acids Res. 2005;33(Database issue):D647-D650. doi:10.1093/nar/gki014
| 2005 | |
houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments Data can be browsed by the type of Alternative Splicing events only. |
62 |
RASE - Recognition of Alternatively Spliced Exonshttp://www.fml.tuebingen.mpg.de/raetsch/RASE |
| Rätsch G, Sonnenburg S, Schölkopf B. RASE: recognition of alternatively spliced exons in C.elegans. Bioinformatics. 2005;21 Suppl 1:i369-i377. doi:10.1093/bioinformatics/bti1053
| 2005 | |
designed to identify and analyze alternatively spliced exons from RNA sequencing (RNA-Seq) data. Returns error 'We are sorry, but that page doesn't exist' as on 30th july 2012 |
63 |
Rescue-ESEhttp://genes.mit.edu/burgelab/rescue-ese/ |
| Fairbrother WG, Yeo GW, Yeh R, et al. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res. 2004;32(Web Server issue):W187-W190. doi:10.1093/nar/gkh393
| 2004 | |
annotates RESCUE-ESE hexamers in vertebrate exons and can be used to predict splicing phenotypes by identifying sequence changes that disrupt or alter predicted ESEs. Gives Exonic Splicing Enhancer motifs. |
64 |
RNAdb - RNA Databasehttp://research.imb.uq.edu.au/rnadb/default.aspx |
| Pang KC, Stephen S, Engström PG, et al. RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res. 2005;33(Database issue):D125-D130. doi:10.1093/nar/gki089
| 2005 | |
contains over 800 unique experimentally studied non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes URL not working as on 14 Dec 2012 |
65 |
Scipiohttp://www.webscipio.org/ |
| Keller O, Odronitz F, Stanke M, Kollmar M, Waack S. Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics. 2008;9:278. Published 2008 Jun 13. doi:10.1186/1471-2105-9-278
| 2008 | |
identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. "Returns message"" Try to lower ""Min. Score"", ""Min. Identity"" and ""BLAT Tilesize"" in the expert options."" when tried multiple times." |
66 |
sgp2http://genome.crg.es/software/sgp2/sgp2.html |
| Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, Guigó R. Comparative gene prediction in human and mouse. Genome Res. 2003;13(1):108-117. doi:10.1101/gr.871403
| 2003 | |
combines ab initio gene prediction with TBLASTX searches between two genome sequences to provide both sensitive and specific gene predictions. "Returns an error :"" cgi-lib.pl: Request to receive too much data: 1858188 bytes"" after multiple tries" |
67 |
Softberryhttp://linux1.softberry.com/berry.phtml |
| Conteduca G, Testa B, Baldo C, et al. Identification of alternative transcripts of NSD1 gene in Sotos Syndrome patients and healthy subjects. Gene. 2023;851:146970. doi:10.1016/j.gene.2022.146970
| 2023 | |
Transcriptional start sites prediction |
68 |
Spideyhttp://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/SpIDey/ |
| Wheelan SJ, Church DM, Ostell JM. Spidey: a tool for mRNA-to-genomic alignments. Genome Res. 2001;11(11):1952-1957. doi:10.1101/gr.195301
| 2001 | |
aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment |
69 |
SpliceIThttp://www.med.auth.gr/research/spliceIT |
| Malousi A, Chouvarda I, Koutkias V, Kouidou S, Maglaveras N. SpliceIT: a hybrid method for splice signal identification based on probabilistic and biological inference. J Biomed Inform. 2010;43(2):208-217. doi:10.1016/j.jbi.2009.09.004
| 2010 | |
method for splice site prediction that couples probabilistic modeling with discriminative computational or experimental features inferred from published studies in two subsequent classification steps |
70 |
SplicePredictorhttp://deepc2.psi.iastate.edu/cgi-bin/sp.cgi |
| Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics. 2004;20(7):1157-1169. doi:10.1093/bioinformatics/bth058
| 2004 | |
predict alternative splicing events by identifying potential splice sites within genomic sequences. 1) Gives information about acceptor and donor site. 2) Gives information about site location and sequence. 3) Also gives information about the site quality. 4) Results can be obtained by e-mail. |
71 |
SpliceScanhttp://stipa.nmsu.edu/SpliceScan/ScoreDonor.html |
| Churbanov A, Rogozin IB, Deogun JS, Ali H. Method of predicting splice sites based on signal interactions. Biol Direct. 2006;1:10. Published 2006 Apr 3. doi:10.1186/1745-6150-1-10
| 2006 | |
outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. URL not working as on 14 Dec 2012 |
72 |
SpliceViewhttp://zeus2.itb.cnr.it/~webgene/wwwspliceview.html |
| Rogozin IB, Milanesi L. Analysis of donor splice sites in different eukaryotic organisms. J Mol Evol. 1997;45(1):50-59. doi:10.1007/pl00006200
| 1997 | |
utilizes sequence data to predict potential splice sites within genes and provides insights into alternative splicing mechanisms The position of acceptor and donor site is given along with intronic and exonic sequence as well as score. |
73 |
Sroogle - Splicing Regulation Online Graphical Enginehttp://sroogle.tau.ac.il/ |
| Schwartz S, Hall E, Ast G. SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res. 2009;37(Web Server issue):W189-W192. doi:10.1093/nar/gkp320
| 2009 | |
makes splicing signal sequence and scoring data available to the biologist in an integrated, visual, easily interpretable, and user-friendly format. 1) Splice site details include element name ( Branch site, Polypyrimidine tract, 3'splice site, 5' splice site), its start and end position and score. 2) Gives splicing regulatory sequences. 3) Also displays matches for mutations. |
74 |
U12DB - U12 Intron Databasehttp://genome.crg.es/cgi-bin/u12db/u12db.cgi |
| Alioto TS. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res. 2007;35(Database issue):D110-D115. doi:10.1093/nar/gkl796
| 2007 | |
aims to catalog the U12-type introns of completely sequenced eukaryotic genomes in a framework that groups orthologous introns with each other 1) Didn't return any results with certain gene names like brca1 or mybl2. 2) Links to UCSC genome Browser is also given. 3) Intronic information is also given, such as junctions and sequence. 4) The donor, acceptor and branch point score is given under splice site details. 5) Gene information gives the description about the gene and the chromosome number. |
75 |
WormBasehttp://www.wormbase.org |
| Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 2001;29(1):82-86. doi:10.1093/nar/29.1.82
| 2001 | |
resource for the Caenorhabditis elegans genome and its biology |
76 |
X:Maphttp://xmap.picr.man.ac.uk |
| Yates T, Okoniewski MJ, Miller CJ. X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res. 2008;36(Database issue):D780-D786. doi:10.1093/nar/gkm779
| 2008 | |
detailed annotation of the intron–exonstructure of each gene, their mappings to known transcripts, and their location relative to Affymetrix exon array target sequences |
77 |
SpliceInfohttp://SpliceInfo.mbc.NCTU.edu.tw/ |
| Huang HD, Horng JT, Lin FM, Chang YC, Huang CC. SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res. 2005;33(Database issue):D80-D85. doi:10.1093/nar/gki129
| 2005 | |
collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 50 -alternative splicing, 30-alternative splicing and intron retention. |
78 |
ProSplicerhttp://bioinfo.csie.ncu.edu.tw/ProSplicer |
| Huang HD, Horng JT, Lee CC, Liu BJ. ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. Genome Biol. 2003;4(4):R29. doi:10.1186/gb-2003-4-4-r29
| 2003 | |
a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. |
79 |
ASDhttp://www.ebi.ac.uk/asd |
| Thanaraj TA, Stamm S, Clark F, Riethoven JJ, Le Texier V, Muilu J. ASD: the Alternative Splicing Database. Nucleic Acids Res. 2004;32(Database issue):D64-D69. doi:10.1093/nar/gkh030
| 2004 | |
committed to maintaining and developing a value-added database of alternative splice events, and of experimentally veri®ed regulatory mechanisms that mediate splice variants |
80 |
ASDhttp://www.ebi.ac.uk/asd |
| Stamm S, Riethoven JJ, Le Texier V, et al. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res. 2006;34(Database issue):D46-D55. doi:10.1093/nar/gkj031
| 2006 | |
systematically collecting and annotating data on alternative splicing |
81 |
ASAP IIhttp://www.bioinformatics.ucla.edu/ASAP2. |
| Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res. 2007;35(Database issue):D93-D98. doi:10.1093/nar/gkl884
| 2006 | |
enabling more detailed exploration of the data, and integrating comparative genomics information with alternative splicing data |
82 |
ASAP ( Alternative Splicing Annotation Project)http://www.bioinformatics.ucla.edu/ASAP |
| Lee C, Atanelov L, Modrek B, Xing Y. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res. 2003;31(1):101-105. doi:10.1093/nar/gkg029
| 2003 | |
provides precise gene exon–intron structure, alternative splicing, tissue specificityof alternative splice forms, and protein isoform sequences resulting from alternative splicing. |
83 |
LivestockExphttps://bioinfo.njau.edu.cn/livestockExp |
| Liu J, Lang K, Tan S, et al. A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals. BMC Genomics. 2022;23(1):706. Published 2022 Oct 17. doi:10.1186/s12864-022-08881-2
| 2022 | |
Database server for the exploration of gene expression and alternative splicing using 43,710 uniformly processed RNA-seq samples from livestock animals |
84 |
AtRTD3 (Arabidopsis thaliana Reference Transcript Database3) |
| Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol. 2022;23(1):149. Published 2022 Jul 7. doi:10.1186/s13059-022-02711-0
| 2022 | |
provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. |
85 |
DEXSeqhttps://bioconductor.org/packages/release/bioc/html/DEXSeq.html; |
| Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012;22(10):2008-2017. doi:10.1101/gr.133744.111
| 2012 | |
designed for the differential analysis of RNA sequencing (RNA-seq) data, specifically to detect differential exon usage. |
86 |
MAJIQ (Modeling Alternative Junction Inclusion Quantification )https://majiq.biociphers.org/ |
| Vaquero-Garcia J, Barrera A, Gazzara MR, et al. A new view of transcriptome complexity and regulation through the lens of local splicing variations. Elife. 2016;5:e11752. Published 2016 Feb 1. doi:10.7554/eLife.11752
| 2016 | |
designed to analyze alternative splicing in RNA-seq data |
87 |
TAPIS ( (Transcriptome Analysis Pipeline for Isoform Sequencing))https://bitbucket.org/comp_bio/tapis/src/master/ |
| Abdel-Ghany SE, Hamilton M, Jacobi JL, et al. A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun. 2016;7:11706. Published 2016 Jun 24. doi:10.1038/ncomms11706
| 2016 | |
process and analyze transcriptome data, particularly focusing on the detection and analysis of alternative splicing events and polyadenylation sites from long-read sequencing data |
88 |
TAMA(Transcriptome Annotation by Modular Algorithms )https://github.com/GenomeRIK/tama |
| Kuo RI, Cheng Y, Zhang R, et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. BMC Genomics. 2020;21(1):751. Published 2020 Oct 30. doi:10.1186/s12864-020-07123-7
| 2020 | |
processing long-read RNA sequencing data, such as Iso-Seq and Nanopore reads. |
89 |
DARTShttps://github.com/Xinglab/DARTS |
| Zhang Z, Pan Z, Ying Y, et al. Deep-learning augmented RNA-seq analysis of transcript splicing. Nat Methods. 2019;16(4):307-310. doi:10.1038/s41592-019-0351-9
| 2019 | |
framework that integrates deep learning-based predictions with empirical RNA-seq evidence to infer differential alternative splicing between biological samples. |
90 |
Pangolinhttps://github.com/tkzeng/Pangolin |
| Zeng T, Li YI. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol. 2022;23(1):103. Published 2022 Apr 21. doi:10.1186/s13059-022-02664-4
| 2022 | |
a deep learning model to predict splice site strength in multiple tissues |
91 |
SpliceAIhttps://github.com/Illumina/SpliceAI |
| de Sainte Agathe JM, Filser M, Isidor B, et al. SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation. Hum Genomics. 2023;17(1):7. Published 2023 Feb 10. doi:10.1186/s40246-023-00451-1
| 2023 | |
free online tool based on the SpliceAI algorithm, and show how it complements the traditional SpliceAI analysis. |
92 |
ECgenehttp://genome.ewha.ac.kr/ECgene/ |
| Kim P, Kim N, Lee Y, Kim B, Shin Y, Lee S. ECgene: genome annotation for alternative splicing. Nucleic Acids Res. 2005;33(Database issue):D75-D79. doi:10.1093/nar/gki118
| 2005 | |
provides annotation for gene structure, function and expression, taking alternative splicing events into consideration. URL working but not leading to any result page after the query has been given. |
93 |
ECgenehttp://genome.ewha.ac.kr/ECgene |
| Lee Y, Lee Y, Kim B, et al. ECgene: an alternative splicing database update. Nucleic Acids Res. 2007;35(Database issue):D99-D103. doi:10.1093/nar/gkl992
| 2006 | |
provide functional annotation for alternatively spliced genes. URL working but not leading to any result page after the query has been given. |
94 |
AS-ALPS (alternative splicing-induced alteration of protein structure)http://genomenetwork.nig.ac.jp/as-alps/ http://as-alps.nagahama-i-bio.ac.jp |
| Shionyu M, Yamaguchi A, Shinoda K, Takahashi K, Go M. AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. Nucleic Acids Res. 2009;37(Database issue):D305-D309. doi:10.1093/nar/gkn869
| 2008 | |
provides information that would be useful for analyzing the effects of alternative splicing (AS) on protein structure, interactions with other biomolecules and protein interaction networks in human and mouse |
95 |
H-DBAS ( Human-transcriptome DataBase for Alternative Splicing)http://jbirc.jbic.or.jp/h-dbas/ |
| Takeda J, Suzuki Y, Nakao M, et al. H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Res. 2007;35(Database issue):D104-D109. doi:10.1093/nar/gkl854
| 2007 | |
each of the alternative splicing (AS) variants corresponds to a completely sequenced and carefully annotated human full-length cDNA, one of those collected for the H-Invitational humantranscriptome annotation meeting. |
96 |
H-DBAShttp://h-invitational.jp/h-dbas/ |
| Takeda J, Suzuki Y, Sakate R, et al. H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic Acids Res. 2010;38(Database issue):D86-D90. doi:10.1093/nar/gkp984
| 2009 | |
database for human alternative splicing (AS) based on H-Invitational full-length cDNAs with correlated RNA-Seq tag information to the AS exons and splice junctions. |
97 |
HOLLYWOODhttp://hollywood.mit.edu. |
| Holste D, Huo G, Tung V, Burge CB. HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res. 2006;34(Database issue):D56-D62. doi:10.1093/nar/gkj048
| 2006 | |
it links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Requires login,but no option to make a new account, so as to login and use the database. |
98 |
MetazExphttps://bioinfo.njau.edu.cn/metazExp |
| Liu J, Yin F, Lang K, et al. MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species. Nucleic Acids Res. 2022;50(D1):D1046-D1054. doi:10.1093/nar/gkab933
| 2021 | |
database for gene expression and alternative splicing profiles based on53 615 uniformly processed publicly available RNAseq samples from 72 metazoan species |
99 |
MAJIQlopediahttps://majiq.biociphers.org/majiqlopedia/ |
| Quesnel-Vallières M, Jewell S, Lynch KW, Thomas-Tikhonenko A, Barash Y. MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer. Nucleic Acids Res. 2024;52(D1):D213-D221. doi:10.1093/nar/gkad1043
| 2023 | |
an encyclopedia of splicing variations that encompasses 86 human tissues and 41 cancer datasets. |
100 |
GTDrifthttps://zenodo.org/records/10527331 |
| Bénitière, F., Duret, L., & Necsulea, A. (2024). GTDrift: A resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes. bioRxiv, 2024-01.
| 2024 | |
enables explorations of genomic and transcriptomic characteristics alongside proxies of the intensity of genetic drift in individual species |
101 |
MAASE(Manually Annotated Alternatively Spliced Events)http://splice.sdsc.edu. |
| Zheng CL, Nair TM, Gribskov M, Kwon YS, Li HR, Fu XD. A database designed to computationally aid an experimental approach to alternative splicing. Pac Symp Biocomput. 2004;78-88. doi:10.1142/9789812704856_0008
| 2004 | |
convenient access, identification, and annotation of alternative splicing events (ASEs) |
102 |
MAASE |
| Zheng CL, Kwon YS, Li HR, et al. MAASE: an alternative splicing database designed for supporting splicing microarray applications. RNA. 2005;11(12):1767-1776. doi:10.1261/rna.2650905
| 2005 | |
specifically designed to support splicing microarray applications |
103 |
ASPicDB (Alternative Splicing Prediction Database)www.caspur.it/ASPicDB |
| Castrignanò T, D'Antonio M, Anselmo A, et al. ASPicDB: a database resource for alternative splicing analysis. Bioinformatics. 2008;24(10):1300-1304. doi:10.1093/bioinformatics/btn113
| 2008 | |
provide access to reliable annotations of the alternative splicing pattern of human genes and to the functional annotation of predicted splicing isoforms. |
104 |
ASPicDBhttp://www.caspur.it/ASPicDB/. |
| Martelli PL, D'Antonio M, Bonizzoni P, et al. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res. 2011;39(Database issue):D80-D85. doi:10.1093/nar/gkq1073
| 2011 | |
provides a unique annotation resource of human protein variants generated by alternative splicing. |
105 |
ASPIChttp://www.caspur.it/ASPIC/ |
| Castrignanò T, Rizzi R, Talamo IG, et al. ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. Nucleic Acids Res. 2006;34(Web Server issue):W440-W443. doi:10.1093/nar/gkl324
| 2006 | |
provides graphical and tabular views of the splicing patterns of all full-length mRNA isoforms compatible with the detected splice sites of genes under investigation as well as relevant structural and functional annotation |
106 |
ASPicDB |
| D'Antonio M, Castrgnanò T, Pallocca M, D'Erchia AM, Picardi E, Pesole G. ASPicDB: a database web tool for alternative splicing analysis. Methods Mol Biol. 2015;1269:365-378. doi:10.1007/978-1-4939-2291-8_23
| 2015 | |
|
107 |
ProSAS (Protein Structure and Alternative Splicing)http://www.bio.ifi.lmu.de/ ProSAS |
| Birzele F, Küffner R, Meier F, Oefinger F, Potthast C, Zimmer R. ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Res. 2008;36(Database issue):D63-D68. doi:10.1093/nar/gkm793
| 2008 | |
provides a unified resource for analyzing effects of alternative splicing events in the context of protein structures |
108 |
AS-CMChttps://www.pmrc.re.kr/ASCMC/ |
| Park J, Lee JO, Lee M, Chung YJ. AS-CMC: a pan-cancer database of alternative splicing for molecular classification of cancer. Sci Rep. 2022;12(1):21074. Published 2022 Dec 6. doi:10.1038/s41598-022-25584-6
| 2022 | |
web-based resource that provides a comprehensive tool to explore the biological implications of AS events, facilitating the discovery of novel AS biomarkers. |
109 |
SpliceWizhttps://github.com/alexchwong/SpliceWiz |
| Wong ACH, Wong JJ, Rasko JEJ, Schmitz U. SpliceWiz: interactive analysis and visualization of alternative splicing in R. Brief Bioinform. 2023;25(1):bbad468. doi:10.1093/bib/bbad468
| 2023 | |
an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. |
110 |
TassDB 2http://www.tassdb.info |
| Sinha R, Lenser T, Jahn N, et al. TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics. 2010;11:216. Published 2010 Apr 29. doi:10.1186/1471-2105-11-216
| 2010 | |
interface to search for specific genes or for genes containing tandem splice sites with specific features |
111 |
TeaAShttp://www.teaas.cn/index.php |
| Mi X, Yue Y, Tang M, et al. TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis). BMC Plant Biol. 2021;21(1):280. Published 2021 Jun 21. doi:10.1186/s12870-021-03065-8
| 2021 | |
provides a comprehensive information on AS by mapping RNA-seq data to the reference genome |
112 |
CuAShttp://cmb.bnu.edu.cn/alt_iso/index.php |
| Sun Y, Zhang Q, Liu B, Lin K, Zhang Z, Pang E. CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. BMC Plant Biol. 2020;20(1):119. Published 2020 Mar 18. doi:10.1186/s12870-020-2312-y
| 2020 | |
database of annotated transcripts generated by alternative splicing in cucumbers that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues |
113 |
MustSeq |
| Mai L, Qiu Y, Lian Z, et al. MustSeq, an alternative approach for multiplexible strand-specific 3' end sequencing of mRNA transcriptome confers high efficiency and practicality. RNA Biol. 2021;18(sup1):232-243. doi:10.1080/15476286.2021.1974208
| 2021 | |
address various aspects of alternative splicing detection and analysis in RNA sequencing data. |
114 |
DeepASmRNA |
| Cao L, Zhang Q, Song H, Lin K, Pang E. DeepASmRNA: Reference-free prediction of alternative splicing events with a scalable and interpretable deep learning model. iScience. 2022;25(11):105345. Published 2022 Oct 14. doi:10.1016/j.isci.2022.105345
| 2022 | |
identify AS transcripts and classify AS events from isoform-level transcriptomic data |
115 |
ASliveASlive.org |
| Liu J, Tan S, Huang S, Huang W. ASlive: a database for alternative splicing atlas in livestock animals. BMC Genomics. 2020;21(1):97. Published 2020 Jan 30. doi:10.1186/s12864-020-6472-9
| 2020 | |
database specifically designed for livestock animals to capture alternative splicing events in heterogeneous samples, which allows users to obtain experimental support of alternative splicing events from a wide range of tissues, cell types, and biological conditions. |
116 |
FishExphttps://bioinfo.njau.edu.cn/fishExp |
| Tan S, Wang W, Jie W, Liu J. FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species. Comput Struct Biotechnol J. 2022;20:3676-3684. Published 2022 Jul 11. doi:10.1016/j.csbj.2022.07.015
| 2022 | |
covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes |
117 |
TCGA SpliceSeqhttp://bioinformatics.mdanderson. org/TCGASpliceSeq |
| Ryan M, Wong WC, Brown R, et al. TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. Nucleic Acids Res. 2016;44(D1):D1018-D1022. doi:10.1093/nar/gkv1288
| 2016 | |
interface for exploring the alternative splicing patterns of TCGA tumors. |
118 |
ASTD (Alternative Splicing Transcript Diversity)http://www.ebi.ac.uk/astd. |
| Koscielny G, Le Texier V, Gopalakrishnan C, et al. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics. 2009;93(3):213-220. doi:10.1016/j.ygeno.2008.11.003
| 2009 | |
gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data |
119 |
PlantExphttps://biotec.njau.edu.cn/plantExp |
| Liu J, Zhang Y, Zheng Y, et al. PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples. Nucleic Acids Res. 2023;51(D1):D1483-D1491. doi:10.1093/nar/gkac917
| 2023 | |
platform for exploration of plant gene expression and alternative splicing profiles based on 131 423 uniformly processed publicly available RNA-seq samples from 85 species in 24 plant orders. |
120 |
PEO: Plant Expression Omnibushttps://expression.plant.tools/ |
| Koh E, Goh W, Julca I, Villanueva E, Mutwil M. PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida. Plant J. 2024;117(5):1592-1603. doi:10.1111/tpj.16566
| 2024 | |
provides biologists with 19 access to gene expression insights across over 100 plant species, ~60,000 manually 20 annotated RNA-seq samples, and more than four million genes |
121 |
CoSIA (Cross-Species Investigation and Analysis)https://github.com/lasseignelab/CoSIA |
| Haldar A, Oza VH, DeVoss NS, Clark AD, Lasseigne BN. CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis. Bioinformatics. 2023;39(12):btad759. doi:10.1093/bioinformatics/btad759
| 2023 | |
allows for relative cross-species comparison of non-diseased wildtype RNA sequencing gene expression data across tissues and species. |
122 |
PastDB (Plant alternative splicing and transcription Data Base)http://pastdb.crg.eu |
| Martín G, Márquez Y, Mantica F, Duque P, Irimia M. Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Genome Biol. 2021;22(1):35. Published 2021 Jan 14. doi:10.1186/s13059-020-02258-y
| 2021 | |
first web resource for A. thaliana integrating gene expression and AS profiles |
123 |
ASpediahttp://combio.snu.ac.kr/aspedia |
| Hyung D, Kim J, Cho SY, Park C. ASpedia: a comprehensive encyclopedia of human alternative splicing. Nucleic Acids Res. 2018;46(D1):D58-D63. doi:10.1093/nar/gkx1014
| 2017 | |
an annotation database, a retrieval system and a browser specialized in the identification of human alternative splicing events. |
124 |
CASAhttp://www.splicedb.net/casa/ |
| Chen Y, Wang G, Li J, et al. CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas. J Transl Med. 2022;20(1):473. Published 2022 Oct 20. doi:10.1186/s12967-022-03699-8
| 2022 | |
platform for studies of AS in COVID-19 and COVID-19-related infectious diseases. |
125 |
MiasDB(http://47.88.84.236/Miasdb |
| Xing Y, Zhao X, Yu T, et al. MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs. PLoS One. 2016;11(5):e0155443. Published 2016 May 11. doi:10.1371/journal.pone.0155443
| 2016 | |
provides a description of molecular interactions associated with human AS events |
126 |
PALS dbhttp://palsdb.ym.edu.tw/ |
| Huang YH, Chen YT, Lai JJ, Yang ST, Yang UC. PALS db: Putative Alternative Splicing database. Nucleic Acids Res. 2002;30(1):186-190. doi:10.1093/nar/30.1.186
| 2002 | |
collection of Putative Alternative Splicing information from 19 936 human UniGene clusters and 16 615 mouse UniGene clusters |
127 |
ASIP(Alternative Splicing in Plants) www.plantgdb.org |
| Wang BB, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A. 2006;103(18):7175-7180. doi:10.1073/pnas.0602039103
| 2006 | |
compile and visualize the evidence for alternative splicing in plants |
128 |
LncAS2Cancer:https://lncrna2as.cd120.com/. |
| Deng Y, Luo H, Yang Z, Liu L. LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers. Brief Bioinform. 2021;22(3):bbaa179. doi:10.1093/bib/bbaa179
| 2020 | |
first comprehensive resource for splicing patterns of lncRNAs in human cancers |
129 |
LncSEA 2.0(http://bio.liclab.net/LncSEA/index.php), |
| Zhang G, Song C, Fan S, et al. LncSEA 2.0: an updated platform for long non-coding RNA related sets and enrichment analysis. Nucleic Acids Res. 2024;52(D1):D919-D928. doi:10.1093/nar/gkad1008
| 2024 | |
updated version of the LncSEA tool, which is designed to annotate long non-coding RNAs (lncRNAs) and investigate their potential roles in splicing regulation and gene expression |
130 |
AVATARhttp://avatar.iecs.fcu.edu.tw/ |
| Hsu FR, Chang HY, Lin YL, et al. AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs. Bioinformation. 2005;1(1):16-18. Published 2005 Apr 22. doi:10.6026/97320630001016
| 2005 | |
database for documenting AS using 5,469,433 human EST sequences and 26,159 human mRNA sequences URL not working as on 14 Dec 2012 |
131 |
EuSplicehttp://66.170.16.154/EuSplice |
| Bhasi A, Pandey RV, Utharasamy SP, Senapathy P. EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics. 2007;23(14):1815-1823. doi:10.1093/bioinformatics/btm084
| 2007 | |
provides reliable splicing information for protein-coding genes of the following 23 eukaryote genomes URL not working as on 14 Dec 2012 |
132 |
FungiExphttps://bioinfo.njau.edu.cn/fungiExp. |
| Liu J, Zhang Y, Shi Y, et al. FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing. Bioinformatics. 2023;39(1):btad042. doi:10.1093/bioinformatics/btad042
| 2023 | |
query and visualize gene expression and alternative splicing in the collected RNA-seq samples |
133 |
OncoSplicingwww.oncosplicing.com |
| Zhang Y, Yao X, Zhou H, et al. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Res. 2022;50(D1):D1340-D1347. doi:10.1093/nar/gkab851
| 2021 | |
for visualization of survival-associated and differential alternative splicing in 2019. |
134 |
SASDt http://bioinfo.hsc.unt.edu/sasd |
| Zhang F, Drabier R. SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics. BMC Bioinformatics. 2013;14 Suppl 14(Suppl 14):S13. doi:10.1186/1471-2105-14-S14-S13
| 2013 | |
o identify, analyze, and characterize novel Exon Skipping and Intron Retention protein isoforms from mass spectrometry and interpret them at the context of pathway, disease, drug and organ specificity or custom gene set with maximum coverage and exclusive focus on alternative splicing |
135 |
MeDAS (Metazoan Developmental Alternative Splicing database)https://das.chenlulab.com |
| Li Z, Zhang Y, Bush SJ, et al. MeDAS: a Metazoan Developmental Alternative Splicing database. Nucleic Acids Res. 2021;49(D1):D144-D150. doi:10.1093/nar/gkaa886
| 2020 | |
provide quantitative data on alternative splicing events |
136 |
ASMDhttp://mco321125.meduo hio.edu/~jbechtel/asmd/ |
| Bechtel JM, Rajesh P, Ilikchyan I, et al. The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence. BMC Res Notes. 2008;1:3. doi:10.1186/1756-0500-1-3
| 2008 | |
a repository for all exonic mutations not associated with splicing junctions that measurably change the pattern of alternative splicing. |
137 |
PlantSPEADhttp://chemyang.ccnu.edu.cn/ccb/database/PlantSPEAD or http://agroda.gzu.edu.cn:9999/ccb/database/PlantSPEAD. |
| Chen MX, Mei LC, Wang F, et al. PlantSPEAD: a web resource towards comparatively analysing stress-responsive expression of splicing-related proteins in plant. Plant Biotechnol J. 2021;19(2):227-229. doi:10.1111/pbi.13486
| 2020 | |
repository of plant SRP classification, annotation, isoform collection and expression analysis |
138 |
QuantAS |
| Song YC, Chen MX, Zhang KL, Reddy ASN, Cao FL, Zhu FY. QuantAS: a comprehensive pipeline to study alternative splicing by absolute quantification of splice isoforms. New Phytol. 2023;240(3):928-939. doi:10.1111/nph.19193
| 2023 | |
tool for addressing the complexities of isoform identification arising from various splicing events |
139 |
DIGGERhttps://exbio.wzw.tum.de/digger |
| Louadi Z, Yuan K, Gress A, et al. DIGGER: exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Res. 2021;49(D1):D309-D318. doi:10.1093/nar/gkaa768
| 2020 | |
database and web tool to study the impact of AS on PPIs |
140 |
ASpedia-Rhttps://github.com/ncc-bioinfo/ASpedia-R. |
| Hyung D, Cho SY, Lee K, Yu N, Hong S, Park C. ASpedia-R: a package to retrieve junction-incorporating features and knowledge-based functions of human alternative splicing events. Bioinform Adv. 2024;4(1):vbae071. Published 2024 May 11. doi:10.1093/bioadv/vbae071
| 2024 | |
interrogate junction-incorporating sequence features for human genes. |
141 |
Splitpea (SPLicing InTeractions PErsonAlized),https://github.com/ylaboratory/splitpea |
| Dannenfelser R, Yao V. Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancer. Pac Symp Biocomput. 2024;29:579-593.
| 2023 | |
approach which characterize PPIs likely disrupted or possibly even increased due to splicing events for individual TCGA cancer patient samples relative to a matched GTEx normal tissue background. |
142 |
CanIsoNethttps://www.caniso.net. |
| Karakulak T, Szklarczyk D, Saylan CC, Moch H, von Mering C, Kahraman A. CanIsoNet: a database to study the functional impact of isoform switching events in diseases. Bioinform Adv. 2023;3(1):vbad050. Published 2023 Apr 17. doi:10.1093/bioadv/vbad050
| 2023 | |
a database to view, browse and search isoform switching events in diseases. |
143 |
APPRIShttp://appris.bioinfo.cnio. es |
| Rodriguez JM, Maietta P, Ezkurdia I, et al. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. 2013;41(Database issue):D110-D117. doi:10.1093/nar/gks1058
| 2013 | |
a database that houses annotations of human splice isoforms. provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation |
144 |
AsMamDBhttp://166.111.30.65/ASMAMDB.html |
| Ji H, Zhou Q, Wen F, Xia H, Lu X, Li Y. AsMamDB: an alternative splice database of mammals. Nucleic Acids Res. 2001;29(1):260-263. doi:10.1093/nar/29.1.260
| 2001 | |
facilitate the systematic study of alternative spliced genes of mammals |
145 |
CancerSplicingQTLhttp://www.cancersplicingqtl-hust.com/ |
| Tian J, Wang Z, Mei S, et al. CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer. Nucleic Acids Res. 2019;47(D1):D909-D916. doi:10.1093/nar/gky954
| 2019 | |
Identification of splicing quantitative trait loci |
146 |
ExonSkipDBhttps://ccsm.uth.edu/ExonSkipDB/ |
| Kim P, Yang M, Yiya K, Zhao W, Zhou X. ExonSkipDB: functional annotation of exon skipping event in human. Nucleic Acids Res. 2020;48(D1):D896-D907. doi:10.1093/nar/gkz917
| 2019 | |
Unique resource for cancer and drug research communities to identify therapeutically targetable exon skipping events. |
147 |
ExonSkipAD (Exon skipping annotation database)https://ccsm.uth.edu/ExonSkipAD. |
| Yang M, Ke Y, Kim P, Zhou X. ExonSkipAD provides the functional genomic landscape of exon skipping events in Alzheimer's disease. Brief Bioinform. 2021;22(5):bbaa438. doi:10.1093/bib/bbaa438
| 2021 | |
provide a resource/reference for functional annotation of ES events in AD and identify therapeutic targets in exon units |
148 |
SpliceAid 2http://www.introni.it/spliceaid.html |
| Piva F, Giulietti M, Burini AB, Principato G. SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum Mutat. 2012;33(1):81-85. doi:10.1002/humu.21609
| 2011 | |
useful to foresee the splicing pattern alteration, to guide the identification of the molecular effect due to the mutations and to understand the tissue-specific alternative splicing |
149 |
SpliceAid-Fhttp://www.caspur.it/SpliceAidF/ |
| Giulietti M, Piva F, D'Antonio M, et al. SpliceAid-F: a database of human splicing factors and their RNA-binding sites. Nucleic Acids Res. 2013;41(Database issue):D125-D131. doi:10.1093/nar/gks997
| 2012 | |
provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements. |
150 |
SpliceAidhttp://www.introni.it/splicing.html |
| Piva F, Giulietti M, Nocchi L, Principato G. SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans. Bioinformatics. 2009;25(9):1211-1213. doi:10.1093/bioinformatics/btp124
| 2009 | |
collecting all the experimentally assessed target RNA sequences that are bound by splicing proteins in humans |
151 |
SpliceDisease databasehttp://cmbi.bjmu.edu.cn/sdisease. |
| Wang J, Zhang J, Li K, Zhao W, Cui Q. SpliceDisease database: linking RNA splicing and disease. Nucleic Acids Res. 2012;40(Database issue):D1055-D1059. doi:10.1093/nar/gkr1171
| 2012 | |
provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. |
152 |
DBASShttps://www.dbass.org.uk/ |
| Buratti E, Chivers M, Hwang G, Vorechovsky I. DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites. Nucleic Acids Res. 2011;39(Database issue):D86-D91. doi:10.1093/nar/gkq887
| 2010 | |
database that provides comprehensive repositories of new exon boundaries induced by pathogenic mutations in human disease genes. |
153 |
EDAShttp://www.genebee.msu.ru/edas/ |
| Nurtdinov RN, Neverov AD, Mal'ko DB, et al. Biofizika. 2006;51(4):589-592.
| 2006 | |
EST-derived alternative splicing database |
154 |
HYBRIDdbhttp://www.primate.or.kr/hybriddb. |
| Kim DS, Huh JW, Kim HS. HYBRIDdb: a database of hybrid genes in the human genome. BMC Genomics. 2007;8:128. Published 2007 May 23. doi:10.1186/1471-2164-8-128
| 2007 | |
designed to detect all of the human hybrid genes (chromosomal-mediated translocation, intergenic splicing-mediated, and few trans-splicing hybrid genes) from publicly available transcript sequences for the understanding of the complex gene catalog in normal and abnormal human tissues |
155 |
TFClass(http://tfclass.bioinf.med.uni-goettingen. de/) |
| Wingender E, Schoeps T, Dönitz J. TFClass: an expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 2013;41(Database issue):D165-D170. doi:10.1093/nar/gks1123
| 2012 | |
provides a comprehensive classification of human transcription factors based on their DNA-binding domains. |
156 |
PASDB (Plant Alternative Splicing Database)http://pasdb.genomics.org.cn |
| Zhou Y, Zhou C, Ye L, et al. Database and analyses of known alternatively spliced genes in plants. Genomics. 2003;82(6):584-595. doi:10.1016/s0888-7543(03)00204-0
| 2003 | |
define collection of 168 genes reported to be alternatively spliced in plants, spanning 44 plant species |
157 |
SpliceMinerhttp://discover.nci.nih.gov/spliceminer |
| Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN. SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. BMC Bioinformatics. 2007;8:75. Published 2007 Mar 5. doi:10.1186/1471-2105-8-75
| 2007 | |
used quickly and easily to check for possible splice variant issues. 1) Gene information includes chromosome number, start and end position, strand information. 2) Probe information includes Probe position. |
158 |
STEPshttp://dbstep.genes.org.uk/ |
| Raistrick CA, Day IN, Gaunt TR. Genome-wide data-mining of candidate human splice translational efficiency polymorphisms (STEPs) and an online database. PLoS One. 2010;5(10):e13340. Published 2010 Oct 11. doi:10.1371/journal.pone.0013340
| 2010 | |
provides a resource for further follow-up of the novel genetic mechanism of splice translational efficiency polymorphisms |
159 |
ssSNPTargethttp://variome.kobic.re.kr/ssSNPTarget/ or http://ssSNPTarget.org. |
| Yang JO, Kim WY, Bhak J. ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database. Hum Mutat. 2009;30(12):E1010-E1020. doi:10.1002/humu.21128
| 2009 | |
provide ssSNPs on human and mouse genes. It includes: 1) ssSNP distribution information in human and mouse genes; 2) effects of SNPs in splice sites: junction strength change, protein domain change, and alternative splicing events (exon skipping, 5'- or 3'-exon extension); 3) splice site conservation in eukaryotes; and 4) associated disease information derived from OMIM, GAD, and HGMD |
160 |
PlaASDBhttp://zzdlab.com/PlaASDB/ASDB/index.html |
| Guo X, Wang T, Jiang L, Qi H, Zhang Z. PlaASDB: a comprehensive database of plant alternative splicing events in response to stress. BMC Plant Biol. 2023;23(1):225. Published 2023 Apr 27. doi:10.1186/s12870-023-04234-7
| 2023 | |
Collected 3,255 RNA-seq data under biotic and abiotic stresses from two important model plants (Arabidopsis and rice) |
161 |
TSVdbhttp://www.tsvdb.com |
| Sun W, Duan T, Ye P, et al. TSVdb: a web-tool for TCGA splicing variants analysis. BMC Genomics. 2018;19(1):405. Published 2018 May 29. doi:10.1186/s12864-018-4775-x
| 2018 | |
A web tool for TCGA alternative splicing variant analysis from 30 clinical variables from 33 tumors |
162 |
IsoVishttps://isomix.org/isovis/. |
| Wan CY, Davis J, Chauhan M, et al. IsoVis - a webserver for visualization and annotation of alternative RNA isoforms. Nucleic Acids Res. Published online May 6, 2024. doi:10.1093/nar/gkae343
| 2024 | |
a freely available webserver that accepts user-supplied transcriptomic data and visualizes the expressed isoforms in a clear, intuitive manner |
163 |
VastDBhttp://vastdb.crg.eu |
| Tapial J, Ha KCH, Sterne-Weiler T, et al. An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Res. 2017;27(10):1759-1768. doi:10.1101/gr.220962.117
| 2017 | |
vertebrate alternate splicing tools and database. Largest resource of genome-wide, quantitative profiles of AS |
164 |
dbSNPhttp://www.ncbi.nlm.nih.gov/snp |
| Day IN. dbSNP in the detail and copy number complexities. Hum Mutat. 2010;31(1):2-4. doi:10.1002/humu.21149
| 2009 | |
summarizes several alternative splicing-related diseases, including cancers and their target genes. |
165 |
FAST DBhttp://193.48.40.18/fastdb |
| Lerivray, H., Méreau, A., & Osborne, H. B. (2006). Our favourite alternative splice site. Biology of the Cell, 98(5), 317-321.
| 2012 | |
(Friendly Alternative Splicing and Transcripts DataBase. |
166 |
HExDBhttp://genomeinfo.org/journal/view.php?number=423 |
| Park¹, J., Lee¹, M., Kim, T. H., & Bhak, J. (2005). HExDB: Human EXon DataBase for Alternative Splicing Pattern Analysis and predicted human gene number. Genomics & Informatics, 3(3), 112-117.
| 2005 | |
Human EXon DataBase for Alternative Splicing Pattern Analysis and predicted human gene number |
167 |
HASDBhttp://www.bioinformatics.ucla.edu/HASDB. |
| Modrek, B., Resch, A., Grasso, C., & Lee, C. (2001). Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic acids research, 29(13), 2850-2859.
| 2001 | |
wide detection of alternative splicing in expressed sequences of human genes |
168 |
MutSpliceDBhttps://brb.nci.nih.gov/splicing |
| Palmisano, A., Vural, S., Zhao, Y., & Sonkin, D. (2021). MutSpliceDB: A database of splice sites variants with RNA‐seq based evidence on effects on splicing. Human mutation, 42(4), 342-345.
| 2023 | |
A database of splice sites variants with RNA-seq based evidence on effects on splicing |
169 |
DBATEhttp://bioinformatica.uniroma2.it/DBATE/ |
| Bianchi, V., Colantoni, A., Calderone, A., Ausiello, G., Ferre, F., & Helmer-Citterich, M. (2013). DBATE: database of alternative transcripts expression. Database, 2013, bat050.
| 2018 | |
Systematic evaluation of isoform function in literature reports of alternative splicing |
170 |
MIsoMinehttp://guanlab.ccmb.med.umich.edu/misomine/ |
| Li, H. D., Omenn, G. S., & Guan, Y. (2015). MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse. Database, 2015, bav045.
| 2015 | |
a high-resolution portal to multiple levels of functional information of alternatively spliced isoforms in the mouse |
171 |
ASDBhttp://cbcg.nerc.gov/asdb |
| Dralyuk,I., Brudno,M., Gelfand,M.S., Zorn,M. and Dubchak,I. (2000) ASDB: database of alternatively spliced genes. Nucleic Acids Res., 28, 296–297.
| 2000 | |
contains 1922 protein and 2486 DNA sequences. |
172 |
GRSDBhttp://bioinformatics.rampo.edu/grsd/ |
| R. Kostadinov, N. Malhotra, M. Viotti, R. Shine, L. D'Antonio, and P. Bagga, 'GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences,' Nucleic Acids Research, vol. 34, pp. D119–124, 2006.
| 2006 | |
database for quadruplex forming g-rich sequences in alternative splicing sequences |
173 |
PolyA_DBhttp://polya.umdnj.edu/polyadb |
| Zhang, H., Hu, J., Recce, M., & Tian, B. (2005). PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic acids research, 33(suppl_1), D116-D120.
| 2005 | |
provide several types of information regarding polyadenylation in mammalian species: URL not working as on 14 Dec 2012 |
174 |
PEIJ_PIEJ DB ( putative exon-intron junction and putative intron-exon junction database)https://sourceforge.net/projects/peijpiej. , https://doi.org/10.21203/rs.3.rs-1979709/v1 |
| Hong, X. (2022). PEIJ_PIEJ DB: A Putative Database for Intron Retention.
| 2022 | |
involving intron retention events from highthroughput experimental datasets such as proteomics datasets and next generation sequencing ones. |
175 |
PEEJ DB (putative exon-exon junction database)http://www.biomedcentral.com/1471-2105/9/537 |
| Mo, F., Hong, X., Gao, F., Du, L., Wang, J., Omenn, G. S., & Lin, B. (2008). A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC bioinformatics, 9(1), 1-8.
| 2008 | |
specified for putative exon skipping events in all kinds of alternative splicing studies |
176 |
ASHESdbhttp://sege.ntu.edu.sg/wester/ashes/ |
| Sakharkar, M. K., Perumal, B. S., Lim, Y. P., Chern, L. P., Yu, Y., & Kangueane, P. (2005). Alternatively spliced human genes by exon skipping–a database (ASHESdb). In silico biology, 5(3), 221-225.
| 2005 | |
available for the human genome data. 1,229 human genes are identified to exhibit alternative splicing by exon skipping. |
177 |
DBASS5http://www.dbass.org.uk/ |
| Buratti E, Chivers M, Hwang G, Vorechovsky I. DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites. Nucleic AcIDs Res. 2011 Jan;39(Database issue):D86-91. Epub 2010 Oct 6. PubMed PMID: 20929868; PubMed Central PMCID: PMC3013770.
| 2010 | |
A database of aberrant 5' splice sites |
178 |
DBASS3http://www.dbass.org.uk/ |
| Buratti E, Chivers M, Hwang G, Vorechovsky I. DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites. Nucleic AcIDs Res. 2011 Jan;39(Database issue):D86-91. Epub 2010 Oct 6. PubMed PMID: 20929868; PubMed Central PMCID: PMC3013770.
| 2010 | |
A database of aberrant 3' splice sites |
179 |
Splice-mediated Variants of Proteins (SpliVaP)http://www.bioinformatica.crs4.org/tools/dbs/splivap/ |
| M. Floris, M. Orsini, and T. A. Thanaraj, 'Splice-mediated variants of proteins (SpliVaP)—data and characterization of changes in signatures among protein isoforms due to alternative splicing,' BMC Genomics, vol. 9, article 453, 2008.
| 2008 | |
reports differences in protein signatures among human splice-mediated protein isoform sequences. |
180 |
SpliceProthttp://lbbc.inca.gov.br/spliceprot. |
| Tavares, R., de Miranda Scherer, N., Pauletti, B. A., Araújo, E., Folador, E. L., Espindola, G., ... & Passetti, F. (2014). SpliceProt: a protein sequence repository of predicted human splice variants. Proteomics, 14(2-3), 181-185.
| 2014 | |
protein sequence repository of transcriptome experimental data used to investigate for putative splice variants in human proteomes. |
181 |
EXPANSIONhttps://expansion.bioinfolab.sns.it/ |
| Arora, C., De Oliveira Rosa, N., Matic, M., Cascone, M., Miglionico, P., & Raimondi, F. (2023). EXPANSION: a webserver to explore the functional consequences of protein-coding alternative splice variants in cancer genomics. Bioinformatics Advances, 3(1), vbad135.
| 2023 | |
web-server to explore the functional consequences of protein-coding alternative splice variants |
182 |
DEDBhttp://proline.bic.nus.edu.sg/dedb/index.htm |
| Lee,B.T., Tan,T.W. and Ranganathan,S. (2004) DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics, 5, 189.
| 2004 | |
contains alternative splicing information organized as splicing graphs, where all transcripts arising from a single gene are collected, organized and classified |
183 |
Alternative Exon Database |
| Stamm,S., Zhu,J., Nakai,K., Stoilov,P. Stoss,O. and Zhang,M.Q. (2000) An alternative-exon database and its statistical analysis. DNA Cell Biol., 19, 739±756.
| 2000 | |
database of alternatively spliced exons that is based on sequences published in the literature |
184 |
EASED (Extended Alternatively Spliced EST Database)http://eased.bioinf.mdc-berlin.de/ |
| Pospisil,H., Herrmann,A., Bortfeldt,R.H. and Reich,J.G. (2004) EASED: Extended Alternatively Spliced EST Database. Nucleic Acids Res., 32, D70–D74.
| 2004 | |
|
185 |
ASHESdbhttp://sege.ntu.edu.sg/wester/ashes/. |
| Sakharkar MK, Perumal BS, Lim YP, Chern LP, Yu Y, Kangueane P. Alternatively spliced human genes by exon skipping--a database (ASHESdb). In Silico Biol. 2005;5(3):221-5. Epub 2004 Dec 8. PMID: 15984933.
| 2005 | |
used to study the impact of alternative splicing on protein function |
186 |
ASP (Alternatively Spliced Protein forms)www.bioinformatics.ucla.edu/ASP |
| Resch, A., Xing, Y., Modrek, B., Gorlick, M., Riley, R., & Lee, C. (2004). Assessing the impact of alternative splicing on domain interactions in the human proteome. Journal of proteome research, 3(1), 76-83.
| 2004 | |
provides a proteom e-wide sam ple of the functional im pact of alternative splicing |
187 |
TCOF1www.genoma.ib.usp.br/TCOF1_database |
| Splendore, A., Fanganiello, R. D., Masotti, C., Morganti, L. S., & Rita Passos‐Bueno, M. (2005). TCOF1 mutation database: novel mutation in the alternatively spliced exon 6A and update in mutation nomenclature. Human mutation, 25(5), 429-434.
| 2005 | |
database of TCOF1 mutations in which all the reported mutations are renamed according to standard recommendations and in reference to the genomic and novel cDNA reference sequences |
188 |
SpliceDB - Splice Databasehttp://www.softberry.com/spldb/SpliceDB.html |
| Burset M, Seledtsov IA, Solovyev VV. SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic AcIDs Res. 2001 Jan 1;29(1):255-9. PubMed PMID: 11125105; PubMed Central PMCID: PMC29840.
| 2001 | |
database of known mammalian splice site sequences |
189 |
Xprohttp://origin.bic. nus.edu.sg/xpro |
| Gopalan, V., Tan, T. W., Lee, B. T., & Ranganathan, S. (2004). Xpro: database of eukaryotic protein‐encoding genes. Nucleic acids research, 32(suppl_1), D59-D63.
| 2004 | |
contains all the eukaryotic protein-encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture URL not working as on 13 Dec 2012 |
190 |
SEDBhttp://glinka.bio.neu.edu/SEDB/SEDB.html |
| Leslin, C. M., Abyzov, A., & Ilyin, V. A. (2004). Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. Bioinformatics, 20(11), 1801-1803.
| 2004 | |
application that allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and the intron phase onto a multiple structural alignment |
191 |
Information for the Coordinates of Exons (ICE) |
| Chong, A., Zhang, G., & Bajic, V. B. (2004). Information for the Coordinates of Exons (ICE): a human splice sites database. Genomics, 84(4), 762-766.
| 2004 | |
Information for the Coordinates of Exons (ICE), of genomic splice sites (SSs) for 10,803 human genes. |
192 |
ASToolhttp://zzdlab.com/ASTool/index.php |
| Qi, H., Guo, X., Wang, T., & Zhang, Z. (2022). ASTool: an easy-to-use tool to accurately identify alternative splicing events from plant RNA-Seq data. International Journal of Molecular Sciences, 23(8), 4079.
| 2022 | |
for detecting AS events from plant RNA-Seq data. |
193 |
MkcDBGAShttp://cmb.bnu.edu.cn/mkcDBGAS/index.php/download |
| Zhang, Q., Cao, L., Song, H., Lin, K., & Pang, E. (2023). MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome. Briefings in Bioinformatics, 24(6), bbad367.
| 2023 | |
first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone |
194 |
GeneSplicer |
| Pertea, M., Lin, X., & Salzberg, S. L. (2001). GeneSplicer: a new computational method for splice site prediction. Nucleic acids research, 29(5), 1185-1190.
| 2001 | |
Detects splice site in genomic DNA of various eukaryotes "1) Results can be obtained by E-mail. 2) Returns an error ""Use of uninitialized value in string eq at /export/www/cgi-bin/cbcb/genesplicer/gspl_cgi.cgi line 162, line 162."" after multiple tries" |
195 |
SpliceMachinehttp://www.bioinformatics.psb.ugent.be/supplementary_data/ |
| Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., & Van de Peer, Y. (2005). SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinformatics, 21(8), 1332-1338.
| 2005 | |
recognizes splice sites based on the positional, compositional and codon bias information that is extracted from a large local context around each candidate splice site |
196 |
QPALMAhttp://www.fml.mpg.de/raetsch/projects/qpalma. |
| De Bona, F., Ossowski, S., Schneeberger, K., & Rätsch, G. (2008). Optimal spliced alignments of short sequence reads. Bioinformatics, 24(16), i174-i180.
| 2008 | |
for computing accurate spliced alignments |
197 |
SplitSeekhttp://solidsoftwaretools.com/gf/project/splitseek |
| Ameur, A., Wetterbom, A., Feuk, L., & Gyllensten, U. (2010). Global and unbiased detection of splice junctions from RNA-seq data. Genome biology, 11, 1-9.
| 2010 | |
designed for the de novo detection of splice junctions in RNA sequencing (RNA-seq) data. |
198 |
SOAPsplicehttp://soap.genomics.org.cn/soapsplice.html. |
| Huang, S., Zhang, J., Li, R., Zhang, W., He, Z., Lam, T. W., ... & Yiu, S. M. (2011). SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data. Frontiers in genetics, 2, 46.
| 2011 | |
a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. |
199 |
findAShttps://github.com/aemilius1984/findAS |
| Potenza, E., Racchi, M. L., Sterck, L., Coller, E., Asquini, E., Tosatto, S. C., ... & Cestaro, A. (2015). Exploration of alternative splicing events in ten different grapevine cultivars. BMC genomics, 16, 1-9.
| 2015 | |
tool to carry out detection of splice variants |
200 |
SUPPAhttps://bitbucket.org/regulatorygenomicsupf/suppa. |
| Alamancos, G. P., Pagès, A., Trincado, J. L., Bellora, N., & Eyras, E. (2015). Leveraging transcript quantification for fast computation of alternative splicing profiles. Rna, 21(9), 1521-1531.
| 2015 | |
calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification |
201 |
PULSEhttp://www.kimlab.org/software/pulse |
| Hao, Y., Colak, R., Teyra, J., Corbi-Verge, C., Ignatchenko, A., Hahne, H., ... & Kim, P. M. (2015). Semi-supervised learning predicts approximately one third of the alternative splicing isoforms as functional proteins. Cell reports, 12(2), 183-189.
| 2015 | |
mapping splicing events to their protein counterparts and the canonical and identification of alternative isoforms |
202 |
NAGNAGhttps://sourceforge.net/projects/nagnag/files/ |
| Yan, X., Sablok, G., Feng, G., Ma, J., Zhao, H., & Sun, X. (2015). nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data. FEBS letters, 589(15), 1766-1770.
| 2015 | |
identifies and quantifies NAGNAG splicing events using RNA-Seq |
203 |
SplicingTypesAnnohttps://sourceforge.net/projects/splicingtypes/files/ OR http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html. |
| Sun, X., Zuo, F., Ru, Y., Guo, J., Yan, X., & Sablok, G. (2015). SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data. Computer Methods and Programs in Biomedicine, 119(1), 53-62.
| 2015 | |
provide annotation for major alternative splicing at exon/intron level. |
204 |
AltAnalyzehttp://www.altanalyze.org/ |
| Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B. R., & Albrecht, M. (2010). AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic acids research, 38(suppl_2), W755-W762.
| 2010 | |
provides a comprehensive software workflow for the statistical and visual analysis of exon expression data |
205 |
DomainGraphhttp://www.domaingraph.de |
| Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, B. R., & Albrecht, M. (2010). AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic acids research, 38(suppl_2), W755-W762.
| 2010 | |
provide an intuitive and comprehensive end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains, microRNA binding sites, molecular interactions and pathways |
206 |
SpliceMap |
| Guo, P., Wang, D., Wu, J., Yang, J., Ren, T., Zhu, B., & Xiang, Y. (2014). The landscape of alternative splicing in cervical squamous cell carcinoma. OncoTargets and therapy, 73-79.
| 2014 | |
used to detect the splicing junctions. |
207 |
VALERIEhttps://cran.r-project.org/web/packages/VALERIE/index.html. |
| Wen, W. X., Mead, A. J., & Thongjuea, S. (2020). VALERIE: visual-based inspection of alternative splicing events at single-cell resolution. PLOS Computational Biology, 16(9), e1008195.
| 2020 | |
R package for visualising alternative splicing events at single-cell resolution. |
208 |
vizAPA: https://github.com/BMILAB/vizAPA. |
| Bi, X., Ye, W., Cheng, X., Yang, N., & Wu, X. (2024). vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data. Bioinformatics, 40(3), btae099.
| 2024 | |
an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. v |
209 |
RNA-Scoophttps://github.com/bcgsc/RNA-Scoop |
| Stephenson, M., Nip, K. M., HafezQorani, S., Gagalova, K. K., Yang, C., Warren, R. L., & Birol, I. (2021). RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes. NAR Genomics and Bioinformatics, 3(4), lqab105.
| 2021 | |
tool to analyze transcript usage across cell categories and clusters |
210 |
SpliceCenterhttp://discover.nci.nih.gov/splicecenter |
| Ryan, M. C., Zeeberg, B. R., Caplen, N. J., Cleland, J. A., Kahn, A. B., Liu, H., & Weinstein, J. N. (2008). SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC bioinformatics, 9, 1-12.
| 2008 | |
suite of web-based tools for identifying the alternative transcripts targeted by contemporary technologies 1) Gene information includes the chromosome number, strand, start, stop. 2) Peptide check displays the coding sequence for a peptide within splice variant of a gene. 3) Expression- check provides visualization of microarray expression data for a gene 4) Batch tools are also provided. |
211 |
PASShttps://github.com/wupengomics/PASS. |
| Wu, P., Pu, L., Deng, B., Li, Y., Chen, Z., & Liu, W. (2019). PASS: A proteomics alternative splicing screening pipeline. Proteomics, 19(13), 1900041.
| 2019 | |
comprehensively detect AS events for the proteomics mass spectrometry (MS) data. |
212 |
ASGAL (Alternative Splicing Graph ALigner)http://asgal.algolab.eu |
| Denti, L., Rizzi, R., Beretta, S., Vedova, G. D., Previtali, M., & Bonizzoni, P. (2018). ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. BMC bioinformatics, 19, 1-21.
| 2018 | |
a tool for mapping RNA-Seq data to the splicing graph, with the specific goal of detecting novel splicing events, involving either annotated or unannotated splice sites. |
213 |
ASimulatoRhttps://github.com/biomedbigdata/ASimulatoR |
| Manz, Q., Tsoy, O., Fenn, A., Baumbach, J., Völker, U., List, M., & Kacprowski, T. (2021). ASimulatoR: splice-aware RNA-Seq data simulation. Bioinformatics, 37(18), 3008-3010.
| 2021 | |
allows for fine-grained control of AS event distributions in RNA-Seq data simulation. |
214 |
OutSplice |
| Bendik, J., Kalavacherla, S., Webster, N., Califano, J., Fertig, E. J., Ochs, M. F., ... & Guo, T. (2023). OutSplice: A Novel Tool for the Identification of Tumor-Specific Alternative Splicing Events. BioMedInformatics, 3(4), 853-868.
| 2023 | |
useful for the identification of rare splicing events in line with tumor biology. |
215 |
ESGqhttps://github.com/AlgoLab/ESGq. |
| Cozzi, D., Bonizzoni, P., & Denti, L. (2023). ESGq: Alternative Splicing events quantification across conditions based on Event Splicing Graphs. bioRxiv, 2023-07.
| 2023 | |
a novel approach for the quantification of AS events across conditions based on read alignment against Event Splicing Graphs. |
216 |
Alternative Splicing Detection Tool (ASDT)http://aias.biol.uoa.gr/~mtheo |
| Adamopoulos, P. G., Theodoropoulou, M. C., & Scorilas, A. (2018). Alternative Splicing Detection Tool—a novel PERL algorithm for sensitive detection of splicing events, based on next-generation sequencing data analysis. Annals of Translational Medicine, 6(12).
| 2018 | |
an algorithm that is capable of identifying alternative splicing events, including novel ones from high-throughput NGS data. |
217 |
PathwaySplicehttps://bioconductor.org/packages/release/bioc/html/PathwaySplice.html |
| Yan, A., Ban, Y., Gao, Z., Chen, X., & Wang, L. (2018). PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data. Bioinformatics, 34(18), 3220-3222.
| 2018 | |
Performs pathway analysis that explicitly adjusts for the number of exons or junctions associated with each gene |
218 |
SpliceDetectorhttps://www.dropbox.com/s/j5o0og159ig6tej/ SpliceDetector%20Executable%20File.rar?dl=0 |
| Baharlou Houreh, M., Ghorbani Kalkhajeh, P., Niazi, A., Ebrahimi, F., & Ebrahimie, E. (2018). SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs. Scientific Reports, 8(1), 5063.
| 2018 | |
application for detecting alternative splicing events from transcripts in all model organisms. |
219 |
DIEGOwww.bioinf.uni-leipzig.de/Software/DIEGO. |
| Doose, G., Bernhart, S. H., Wagener, R., & Hoffmann, S. (2018). DIEGO: detection of differential alternative splicing using Aitchison’s geometry. Bioinformatics, 34(6), 1066-1068.
| 2017 | |
a compositional data analysis method able to detect DAS between two sets of RNA-Seq samples based on split reads. |
220 |
TSIS (time-series isoform switch)https://github.com/wyguo/TSIS. |
| Guo, W., Calixto, C. P., Brown, J. W., & Zhang, R. (2017). TSIS: an R package to infer alternative splicing isoform switches for time-series data. Bioinformatics, 33(20), 3308-3310.
| 2017 | |
R package, which is the first tool for detecting significant transcript isoform switches in time-series data |
221 |
EventPointer,N/A |
| Romero, J. P., Muniategui, A., De Miguel, F. J., Aramburu, A., Montuenga, L., Pio, R., & Rubio, A. (2016). EventPointer: an effective identification of alternative splicing events using junction arrays. BMC genomics, 17, 1-18.
| 2016 | |
an R package (built under the aroma.affymetrix framework) to search and analyze Alternative Splicing events using HTA 2.0 arrays |
222 |
jSplicehttp://www.mhs.biol.ethz.ch/research/krek/jsplice. |
| Christinat, Y., Pawłowski, R., & Krek, W. (2016). jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data. Bioinformatics, 32(14), 2111-2119.
| 2016 | |
enables de novo extraction of alternative splicing events from RNA-sequencing data with high accuracy, reliability and speed |
223 |
Splicing Expresshttp://www.bioinformatics-brazil.org/splicingexpress. |
| Kroll, J. E., Kim, J., Ohno-Machado, L., & de Souza, S. J. (2015). Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data. PeerJ, 3, e1419.
| 2015 | |
perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms |
224 |
Vials (VIsualizing ALternative Splicing)http://vcglab.org/vials/. |
| Strobelt, H., Alsallakh, B., Botros, J., Peterson, B., Borowsky, M., Pfister, H., & Lex, A. (2015). Vials: visualizing alternative splicing of genes. IEEE transactions on visualization and computer graphics, 22(1), 399-408.
| 2016 | |
enables analysts to explore the various datasets that scientists use to make judgments about isoforms |
225 |
rMATrnaseq-mats.sourceforge.net/ |
| Shen, S., Park, J. W., Lu, Z. X., Lin, L., Henry, M. D., Wu, Y. N., ... & Xing, Y. (2014). rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proceedings of the National Academy of Sciences, 111(51), E5593-E5601.
| 2014 | |
designed for detection of differential alternative splicing from replicate RNA-Seq data. |
226 |
PrimerSeqhttp://primerseq.sourceforge.net/ |
| Tokheim C, Park JW, Xing Y. PrimerSeq: Design and visualization of RT-PCR primers for alternative splicing using RNA-seq data. Genomics Proteomics Bioinformatics. 2014 Apr;12(2):105-9. doi: 10.1016/j.gpb.2014.04.001. Epub 2014 Apr 18. PMID: 24747190; PMCID: PMC4411361.
| 2014 | |
systematic design and visualization of RT-PCR primers using RNA-seq data. |
227 |
AVISPAhttp://avispa.biociphers.org |
| Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ. AVISPA: a web tool for the prediction and analysis of alternative splicing. Genome Biol. 2013;14(10):R114. doi: 10.1186/gb-2013-14-10-r114. PMID: 24156756; PMCID: PMC4014802.
| 2013 | |
tool for splicing prediction and analysis. |
228 |
ExonSuitehttps://github.com/dilanustek/ExonSuite |
| Ustek D, Kohrman A, Krstic B, Fernandez K. ExonSuite: algorithmically optimizing alternative gene splicing for the PUF proteins. Comput Biol Med. 2013 Sep;43(8):1023-4. doi: 10.1016/j.compbiomed.2013.05.014. Epub 2013 May 28. PMID: 23816174.
| 2013 | |
optimize alternative gene splicing for the PUF proteins |
229 |
ASFinderhttp://proteomics.ysu.edu/tools/ASFinder.html |
| Min XJ. ASFinder: a tool for genome-wide identification of alternatively splicing transcripts from EST-derived sequences. Int J Bioinform Res Appl. 2013;9(3):221-6. doi: 10.1504/IJBRA.2013.053603. PMID: 23649736.
| 2013 | |
identify AS isoforms from EST-derived sequences. |
230 |
Alt Event Finder |
| Zhou A, Breese MR, Hao Y, Edenberg HJ, Li L, Skaar TC, Liu Y. Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. BMC Genomics. 2012;13 Suppl 8(Suppl 8):S10. doi: 10.1186/1471-2164-13-S8-S10. Epub 2012 Dec 17. PMID: 23281921; PMCID: PMC3535697.
| 2012 | |
tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and Scripture. |
231 |
PIntronhttp://www.algolab.eu/PIntron |
| Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P. PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. BMC Bioinformatics. 2012 Apr 12;13 Suppl 5(Suppl 5):S2. doi: 10.1186/1471-2105-13-S5-S2. PMID: 22537006; PMCID: PMC3358663.
| 2012 | |
predict the full-length transcript isoforms potentially expressed by the gene and, also include a module for the CDS annotation of the predicted transcripts. |
232 |
SpliceGrapherhttps://splicegrapher.sourceforge.net/ |
| Rogers MF, Thomas J, Reddy AS, Ben-Hur A. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol. 2012 Jan 31;13(1):R4. doi: 10.1186/gb-2012-13-1-r4. PMID: 22293517; PMCID: PMC3334585.
| 2012 | |
predict splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. |
233 |
SplicingViewerhttp://bioinformatics.zj.cn/splicingviewer |
| Liu Q, Chen C, Shen E, Zhao F, Sun Z, Wu J. Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer. Genomics. 2012 Mar;99(3):178-82. doi: 10.1016/j.ygeno.2011.12.003. Epub 2011 Dec 28. PMID: 22226708.
| 2012 | |
detection, annotation and visualization of splice junctions and alternative splicing events from RNA-Seq data |
234 |
HMMSplicerhttp://derisilab.ucsf.edu/software/ hmmsplicer. |
| Dimon,M.T., Sorber,K. and DeRisi,J.L. (2010) HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One, 5, e13875.
| 2010 | |
A tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data |
235 |
SFmap(http://sfmap.technion.ac.il |
| Paz,I., Akerman,M., Dror,I., Kosti,I. and Mandel-Gutfreund,Y. (2010) SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res., 38, W281–W285.
| 2010 | |
A web server for motif analysis and prediction of splicing factor binding sites |
236 |
ISIShttp://isis.bit.uq.edu.au/ |
| Croft,L., Schandorff,S., Clark,F., Burrage,K., Arctander,P. and Mattick,J.S. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat. Genet., 24, 340–341.
| 2000 | |
contains information on over 170,000 spliceosomal introns |
237 |
IsoEMhttp://dna.engr.uconn.edu/software/IsoEM/ |
| Nicolae, M., Mangul, S., Măndoiu, I. I., & Zelikovsky, A. (2011). Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms for molecular biology, 6, 1-13.
| 2011 | |
Tool for the estimation of alternative splicing isoformfrequencies from RNA-Seq data |
238 |
MAISTAShttp://maistas.bioinformatica.crs4.it/. |
| Floris, M., Raimondo, D., Leoni, G., Orsini, M., Marcatili, P., & Tramontano, A. (2011). MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics, 27(12), 1625-1629.
| 2011 | |
A tool for automatic structural evaluation of alternativesplicing products |
239 |
SpliceToolshttps://github.com/flemingtonlab/SpliceTools |
| Flemington, E. K., Flemington, S. A., O’Grady, T. M., Baddoo, M., Nguyen, T., Dong, Y., & Ungerleider, N. A. (2023). SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing. Nucleic Acids Research, 51(7), e42-e42.
| 2023 | |
a suite of data processing modules that arms investigators with the ability to quickly produce summary statistics, mechanistic insights, and functional significance of AS changes through command line or through an online user interface |
240 |
SPLOOCEhttp://www.bioinformatics-brazil.org/splooce |
| Kroll, J. E., Galante, P. A., Ohara, D. T., Navarro, F. C., Ohno-Machado, L., & de Souza, S. J. (2012). SPLOOCE: a new portal for the analysis of human splicing variants. RNA biology, 9(11), 1339-1343.
| 2012 | |
a portal for the analysis of human splicing variants. |
241 |
ASTKhttps://pypi.org/project/astk/ or https://hub.docker.com/r/huangshing/astk |
| Huang, S., He, J., Yu, L., Guo, J., Jiang, S., Sun, Z., ... & Zhang, Y. (2024). ASTK: A Machine Learning‐Based Integrative Software for Alternative Splicing Analysis. Advanced Intelligent Systems, 2300594.
| 2024 | |
a software package covering upstream and downstream analysis of AS |
242 |
BIPASShttp://bip.umiacs.umd.edu:8080/. |
| Lacroix, Z., Legendre, C., Raschid, L., & Snyder, B. (2007). BIPASS: BioInformatics Pipeline Alternative Splicing Services. Nucleic acids research, 35(suppl_2), W292-W296.
| 2007 | |
Bioinformatics pipeline alternative splicing services, designed to exploit scientific workflows and database mediation technology to implement scientific pipelines, and to develop useful tools for the AS community. |
243 |
ExInthttp://intron.bic.nus.edu.sg/exint/newexint/exint.html |
| Sakharkar, M., Passetti, F., de Souza, J. E., Long, M., & de Souza, S. J. (2002). ExInt: an exon intron database. Nucleic acids research, 30(1), 191-194.
| 2002 | |
stores all the information on the GenBank eukaryotic entries containing an annotated intron sequence |
244 |
EIDhttp://mcb.harvard.edu/gilbert/EID |
| Saxonov, S., Daizadeh, I., Fedorov, A., & Gilbert, W. (2000). EID: the Exon–Intron Database—an exhaustive database of protein-coding intron-containing genes. Nucleic acids research, 28(1), 185-190.
| 2000 | |
contains information on protein coding genes along with extensive description of each gene and its DNA and protein sequences, as well as splice motif information. |
245 |
NetUTRhttp://www.cbs.dtu.dk/services/NetUTR/ |
| Eden, E., & Brunak, S. (2004). Analysis and recognition of 5′ UTR intron splice sites in human pre‐mRNA. Nucleic Acids Research, 32(3), 1131-1142.
| 2004 | |
Prediction of splice sites in 5' UTR regions |
246 |
HYBRIDdbhttp://www.primate.or.kr/hybriddb/ |
| Kim, D17519042. S., Huh, J. W., & Kim, H. S. (2007). HYBRIDdb: a database of hybrid genes in the human genome. Bmc Genomics, 8, 1-5.
| 2007 | |
contain comprehensive list of hybrid genes created by trans-splicing, intergenic splicing, and genomic rearrangement between two human genes. |
247 |
IntSplicehttps://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice/ |
| Shibata, A., Okuno, T., Rahman, M. A., Azuma, Y., Takeda, J. I., Masuda, A., ... & Ohno, K. (2016). IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome. Journal of human genetics, 61(7), 633-640.
| 2016 | |
Predict a splicing consequence of SNV |
248 |
IsoFunchttps://guanlab.ccmb.med.umich.edu/isofunc |
| Panwar, B., Menon, R., Eksi, R., Li, H. D., Omenn, G. S., & Guan, Y. (2016). Genome-wide functional annotation of human protein-coding splice variants using multiple instance learning. Journal of proteome research, 15(6), 1747-1753.
| 2016 | |
A tool for assigning function to protein-coding splice variants |
249 |
NetGene2http://www.cbs.dtu.dk/services/NetGene2/ |
| Pertea, M., Lin, X., & Salzberg, S. L. (2001). GeneSplicer: a new computational method for splice site prediction. Nucleic acids research, 29(5), 1185-1190.
| 2001 | |
Splice sites in human, C. elegans and A. thaliana |
250 |
Spliceporthttp://spliceport.cbcb.umd.edu/ |
| Dogan, R. I., Getoor, L., Wilbur, W. J., & Mount, S. M. (2007). SplicePort—an interactive splice-site analysis tool. Nucleic acids research, 35(suppl_2), W285-W291.
| 2007 | |
Splice-site predictions for submitted sequences URL not working as on 14 Dec 2012 |
251 |
FLJ Human cDNA DBhttp://flj.lifesciencedb.jp/top/ |
| Isogai, T., & Wakamatsu, A. Alternative Splicing by Analyzing a Human mRNA Diversity Using Data of FLJ Human cDNAs.
| | |
Variations of transcription start site (TSS) and splicing |
252 |
SimSpliceEvolhttps://github.com/UdeS-CoBIUS/SimSpliceEvol. |
| Kuitche, E., Jammali, S., & Ouangraoua, A. (2019). SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution. BMC bioinformatics, 20, 1-13.
| 2019 | |
simulate the evolution of sets of alternative transcripts along the branches of an input gene tree. |
253 |
MARVEL10.1093/nar/gkac1260 |
| Wen, W. X., Mead, A. J., & Thongjuea, S. (2023). MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data. Nucleic Acids Research, 51(5), e29-e29.
| 2023 | |
a comprehensive R package for single-cell splicing analysis applicable to RNA sequencing generated from the plate- and droplet-based methods |
254 |
ASmodelerhttp://genome. ewha.ac.kr/ECgene/ASmodeler/ |
| Kim, N., Shin, S., & Lee, S. (2004). ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. Nucleic acids research, 32(suppl_2), W181-W186.
| 2004 | |
ASmodeler is a novel web-based utility that finds gene models including alternative splicing events from genomic alignment of mRNA, EST and protein sequences |
255 |
ECgene |
| Kim, N., Shin, S., & Lee, S. (2005). ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome research, 15(4), 566-576.
| 2005 | |
a novel gene-modeling method, ECgene (gene modeling by EST Clustering), which combines genomebased EST clustering and transcript assembly procedure in a coherent and consistent fashion, taking alternative splicing events into account URL working but not leading to any result page after the query has been given. |
256 |
ASePCRhttp://genome.ewha.ac.kr/ ASePCR/ |
| Kim, N., Lim, D., Lee, S., & Kim, H. (2005). ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs. Nucleic acids research, 33(suppl_2), W681-W685.
| 2005 | |
|
257 |
ASGShttp://asgs.biolinfo.org. |
| Bollina, D., Lee, B. T., Tan, T. W., & Ranganathan, S. (2006). ASGS: an alternative splicing graph web service. Nucleic acids research, 34(suppl_2), W444-W447.
| 2006 | |
web service facilitating the systematic study of alternatively spliced genes of higher eukaryotes by generating splicing graphs for the compact visual representation of transcript diversity from a single gene |
258 |
ASTALAVISTA (alternative splicing transcriptional landscape visualization tool)http://genome.imim.es/astalavista |
| Foissac, S., & Sammeth, M. (2007). ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic acids research, 35(suppl_2), W297-W299.
| 2007 | |
allows to dynamically identify, extract and display complex AS events from annotated genes. |
259 |
Splicyhttp://host10.bioinfo3.ifom-ieo-campus.it/splicy/ |
| Rambaldi, D., Felice, B., Praz, V., Bucher, P., Cittaro, D., & Guffanti, A. (2007). Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC bioinformatics, 8, 1-8.
| 2007 | |
generate probeset annotations and images describing the relation between the single probes and intron/exon structure of the target gene |
260 |
AsiDesignerhttp://sysbio.kribb.re.kr/AsiDesigner/. |
| Park, Y. K., Park, S. M., Choi, Y. C., Lee, D., Won, M., & Kim, Y. J. (2008). AsiDesigner: exon-based siRNA design server considering alternative splicing. Nucleic acids research, 36(suppl_2), W97-W103.
| 2008 | |
provides siRNA design capability to account for alternative splicing for mRNA level gene silencing |
261 |
ExoPLOThttp://retrogenomics3.uni-muenster.de:3838/exz-plot-d/ |
| Zhang, F., Raabe, C. A., Cardoso-Moreira, M., Brosius, J., Kaessmann, H., & Schmitz, J. (2022). ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement. Genomics, 114(4), 110434.
| 2022 | |
tool to analyze and visualize the expression of alternatively spliced genes. |
262 |
IsoSplitterhttps://github.com/Hengfu-Yin/IsoSplitter |
| Wang, Y., Hu, Z., Ye, N., & Yin, H. (2021). IsoSplitter: identification and characterization of alternative splicing sites without a reference genome. RNA, 27(8), 868-875.
| 2021 | |
validate AS gene 'split sites' |
263 |
Jutils Toolhttps://github.com/Splicebox/Jutils |
| Yang, G., Cope, L., He, Z., & Florea, L. (2021). Jutils: a visualization toolkit for differential alternative splicing events. Bioinformatics, 37(22), 4272-4274.
| 2021 | |
a toolkit, Jutils, for visualizing differential splicing events at the intron (splice junction) |
264 |
MntJULiPhttps://github.com/splicebox/ |
| Yang, G., Sabunciyan, S., & Florea, L. (2022). Comprehensive and scalable quantification of splicing differences with MntJULiP. Genome biology, 23(1), 195.
| 2022 | |
MntJULiP detects intron-level differences in alternative splicing from RNA-seq data using a Bayesian mixture model. |
265 |
AS-Quant (Alternative Splicing Quantitation)https://github.com/CompbioLabUCF/AS-Quant |
| Fahmi, N. A., Nassereddeen, H., Chang, J., Park, M., Yeh, H., Sun, J., ... & Zhang, W. (2021). As-quant: Detection and visualization of alternative splicing events with rna-seq data. International journal of molecular sciences, 22(9), 4468.
| 2021 | |
a robust program to identify alternative splicing events from RNA-seq data. |
266 |
3D RNA-seqhttps://3drnaseq.hutton.ac.uk/. |
| Guo, W., Tzioutziou, N. A., Stephen, G., Milne, I., Calixto, C. P., Waugh, R., ... & Zhang, R. (2021). 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA biology, 18(11), 1574-1587.
| 2021 | |
pipeline for the comprehensive analysis of RNA-seq data from any organism |
267 |
RNfuzzyApphttps://gitlab.com/habermann_lab/rna-seq-analysis-app |
| Haering, M., & Habermann, B. H. (2021). RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis. F1000Research, 10.
| 2021 | |
software application designed for the analysis of RNA sequencing (RNA-seq) data with a specific focus on identifying and characterizing alternative splicing events using fuzzy logic. |
268 |
EventPointer 3.0(https://bioconductor.org/packages/release/bioc/html/EventPointer.html) |
| Ferrer-Bonsoms, J. A., Gimeno, M., Olaverri, D., Sacristan, P., Lobato, C., Castilla, C., ... & Rubio, A. (2022). EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains. NAR Genomics and Bioinformatics, 4(3), lqac067.
| 2022 | |
comprehensive analysis of alternative splicing events from RNA-seq data |
269 |
rMAPS2http://rmaps.cecsresearch.org/ |
| Hwang, J. Y., Jung, S., Kook, T. L., Rouchka, E. C., Bok, J., & Park, J. W. (2020). rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Research, 48(W1), W300-W306.
| 2020 | |
RNA Map Analysis and Plotting Server 2 |
270 |
MapSplicehttp://www.netlab.uky .edu/p/bioinfo/MapSplice |
| Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., ... & Liu, J. (2010). MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic acids research, 38(18), e178-e178.
| 2010 | |
highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. |
271 |
ExonImpacthttp://watson.compbio.iupui.edu/ExonImpact |
| Li, M., Feng, W., Zhang, X., Yang, Y., Wang, K., Mort, M., ... & Liu, Y. (2017). ExonImpact: prioritizing pathogenic alternative splicing events. Human mutation, 38(1), 16-24.
| 2016 | |
prioritizing and evaluating the functional consequences of hitherto uncharacterized AS event |
272 |
Alternative Splicing Gallery (ASG)http://statgen.ncsu.edu/asg/ |
| Leipzig, J., Pevzner, P., & Heber, S. (2004). The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Research, 32(13), 3977-3983.
| 2004 | |
explore and visualize gene structure and alternative splicing |
273 |
DiffSplicehttp://www.netlab.uky.edu/p/bioinfo/DiffSplice |
| Hu, Y., Huang, Y., Du, Y., Orellana, C. F., Singh, D., Johnson, A. R., ... & Liu, J. (2013). DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic acids research, 41(2), e39-e39.
| 2013 | |
detection and visualization of differential alternative transcription. |
274 |
MATShttp://intron.healthcare.uiowa.edu/MATS/ . |
| Shen, S., Park, J. W., Huang, J., Dittmar, K. A., Lu, Z. X., Zhou, Q., ... & Xing, Y. (2012). MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic acids research, 40(8), e61-e61.
| 2012 | |
a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. |
275 |
SpliceTraphttp://rulai.cshl.edu/splicetrap/. |
| Wu, J., Akerman, M., Sun, S., McCombie, W. R., Krainer, A. R., & Zhang, M. Q. (2011). SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27(21), 3010-3016.
| 2011 | |
a method to quantify exon inclusion levels using paired-end RNA-seq data. |
276 |
ALEXA-seqhttp://www.alexaplatform.org/alexa_seq/. |
| Griffith, M., Griffith, O. L., Mwenifumbo, J., Goya, R., Morrissy, A. S., Morin, R. D., ... & Marra, M. A. (2010). Alternative expression analysis by RNA sequencing. Nature methods, 7(10), 843-847.
| 2010 | |
a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues |
277 |
TAPAShttp://davinci.crg.es/tapas/ |
| Yang, J. S., Sabidó, E., Serrano, L., & Kiel, C. (2014). TAPAS: tools to assist the targeted protein quantification of human alternative splice variants. Bioinformatics, 30(20), 2989-2990.
| 2014 | |
a framework that brings together experimental design and computational analysis for the absolute quantification of splice variants |
278 |
spliceRhttp://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html |
| Vitting-Seerup, K., Porse, B. T., Sandelin, A., & Waage, J. (2014). spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC bioinformatics, 15, 1-7.
| 2014 | |
an R package for classification of alternative splicing and prediction of coding potential. |
279 |
ASSPhttp://es.embnet.org/~mwang/assp.html. |
| Wang, M., & Marín, A. (2006). Characterization and prediction of alternative splice sites. Gene, 366(2), 219-227.
| 2006 | |
a web tool used for predicting alternative splice sites |
280 |
Mixture-of-isoforms (MISO)https://miso.readthedocs.io/en/fastmiso/; |
| Katz, Y., Wang, E. T., Airoldi, E. M., & Burge, C. B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature methods, 7(12), 1009-1015.
| 2010 | |
a statistical model used in the estimation of expression of alternatively spliced exons and isoforms |
281 |
PASA (Program to Assemble Spliced Alignments )http://www.tigr.org/tdb/ e2k1/ath1/pasa_annot_updates/pasa_annot_updates.shtml |
| Haas, B. J., Delcher, A. L., Mount, S. M., Wortman, J. R., Smith Jr, R. K., Hannick, L. I., ... & White, O. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic acids research, 31(19), 5654-5666.
| 2003 | |
gathers and clusters spliced transcript alignments |
282 |
WebScipiohttp://www.webscipio.org. |
| Hatje, K., Hammesfahr, B., & Kollmar, M. (2013). WebScipio: reconstructing alternative splice variants of eukaryotic proteins. Nucleic Acids Research, 41(W1), W504-W509.
| 2014 | |
allows predicting mutually exclusive spliced exons and tandemly arrayed gene duplicates. |
283 |
Alternative Splicing Effects ASsessment Tools (AS-EAST)http://as-alps.nagahama-i-bio.ac.jp/ASEAST/. |
| Shionyu, M., Takahashi, K. I., & Go, M. (2012). AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts. Bioinformatics, 28(15), 2076-2077.
| 2012 | |
tool for the functional annotation of putative proteins encoded by transcripts generated by alternative splicing |
284 |
PRIMEGENS-v2http://primegens.org. |
| Srivastava, G. P., Hanumappa, M., Kushwaha, G., Nguyen, H. T., & Xu, D. (2011). Homolog-specific PCR primer design for profiling splice variants. Nucleic acids research, 39(10), e69-e69.
| 2011 | |
designed for predicting and analyzing alternative splicing events in RNA-seq data. |
285 |
COSIE (Corrected Splicing Indices for Exon arrays)www.fmi.ch/groups/gbioinfo |
| Gaidatzis, D., Jacobeit, K., Oakeley, E. J., & Stadler, M. B. (2009). Overestimation of alternative splicing caused by variable probe characteristics in exon arrays. Nucleic acids research, 37(16), e107-e107.
| 2009 | |
for any given set of new exon array experiments corrects for the observed bias and improves the detection of alternative splicing |
286 |
PASS (Alternative Splicing and Protein Structure Scrutinizer ) |
| D'Antonio, M., & Masseroli, M. (2009). Extraction, integration and analysis of alternative splicing and protein structure distributed information. BMC bioinformatics, 10, 1-12.
| 2009 | |
Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank |
287 |
PASE (Prediction of Alternative Signaling Exons) |
| Leparc, G. G., & Mitra, R. D. (2007). Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic acids research, 35(10), 3192-3202.
| 2007 | |
a computational tool to identify novel alternative cassette exons that code for kinase phosphorylation or signaling protein-binding sites |
288 |
Plant Gene and Alternatively Spliced Variant Annotator (PGAA) |
| Chen, F. C., Wang, S. S., Chaw, S. M., Huang, Y. T., & Chuang, T. J. (2007). PGAA: a plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species EST conservation from seven plant species. Plant Physiology 143, 1086-1095.
| 2007 | |
for gene/AS prediction in the rice genome |
289 |
Alternative Splicing Assembler (ASA) |
| Hui, L., Zhang, X., Wu, X., Lin, Z., Wang, Q., Li, Y., & Hu, G. (2004). Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment. Oncogene, 23(17), 3013-3023.
| 2004 | |
which searched all putative alternative splicing variants through genomic EST alignmen |
290 |
PASSionhttps://trac.nbic.nl/passion OR ftp://ftp.sanger.ac.uk/pub/zn1/passion |
| Zhang, Y., Lameijer, E. W., 't Hoen, P. A., Ning, Z., Slagboom, P. E., & Ye, K. (2012). PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. Bioinformatics, 28(4), 479-486.
| 2012 | |
a pattern growth algorithm-based pipeline for splice site detection in paired-end RNA-Seq reads |
291 |
Asprofile(https://ccb.jhu.edu/software/ASprofile/) |
| Florea, L., Song, L., & Salzberg, S. L. (2013). Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Research, 2.
| 2013 | |
classify and count the AS events in each sample |
292 |
CLASS2http://sourceforge.net/projects/Splicebox. |
| Song, L., Sabunciyan, S., & Florea, L. (2016). CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic acids research, 44(10), e98-e98.
| 2016 | |
assemble likely models of full-length transcripts while capturing local splicing variations with high accuracy, to allow genome and system-wide alternative splicing analyses |
293 |
Diceseqhttp://diceseq.sf.net. |
| Huang, Y., & Sanguinetti, G. (2016). Statistical modeling of isoform splicing dynamics from RNA-seq time series data. Bioinformatics, 32(19), 2965-2972.
| 2016 | |
isoform quantification method tailored to correlated RNA-seq experiments |
294 |
EBChangepoint (empirical Bayes change-point)http://ebchangepoint.sourceforge.net/. |
| Zhang, J., & Wei, Z. (2016). An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing. Bioinformatics, 32(12), 1823-1831.
| 2016 | |
empirical Bayes change-point model to identify alternative 30 SS and 50 SS. |
295 |
Eoulsanhttp://transcriptome.ens.fr/eoulsan/ |
| Jourdren, L., Bernard, M., Dillies, M. A., & Le Crom, S. (2012). Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses. Bioinformatics, 28(11), 1542-1543.
| 2012 | |
Allows automated analysis (mapping, counting and differencial analysis with DESeq2). |
296 |
GESS (graph-based exon-skipping scanner)http://motif.bmi.ohio-state.edu/GESS_Web/ |
| Wang, J., Ye, Z., Huang, T. H., Shi, H., & Jin, V. X. (2017). Computational methods and correlation of exon-skipping events with splicing, transcription, and epigenetic factors. Cancer Gene Networks, 163-170.
| 2017 | |
for de novo detection of exon-skipping event sites from raw RNA-seq reads. |
297 |
LEMONShttp://dx.doi.org/10.6084/m9.figshare.1599765. |
| Levin, L., Bar-Yaacov, D., Bouskila, A., Chorev, M., Carmel, L., & Mishmar, D. (2015). LEMONS–a tool for the identification of splice junctions in transcriptomes of organisms lacking reference genomes. PloS one, 10(11), e0143329.
| 2015 | |
A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes. |
298 |
Rail-RNAhttp://rail.bio. |
| Nellore, A., Collado-Torres, L., Jaffe, A. E., Alquicira-Hernández, J., Wilks, C., Pritt, J., ... & Langmead, B. (2017). Rail-RNA: scalable analysis of RNA-seq splicing and coverage. Bioinformatics, 33(24), 4033-4040.
| 2017 | |
Scalable analysis of RNA-seq splicing and coverage. |
299 |
RSVPhttp://ohlerlab.mdc-berlin.de/software/RSVP/ . |
| Majoros, W. H., Lebeck, N., Ohler, U., & Li, S. (2014). Improved transcript isoform discovery using ORF graphs. Bioinformatics, 30(14), 1958-1964.
| 2014 | |
a software package for prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads |
300 |
SAJR |
| Mazin, P. et al. Widespread splicing changes in human brain development and aging. Mol. Syst. Biol. 9, 633 (2013).
| 2013 | |
designed for analyzing alternative splicing events using RNA-Seq data |
301 |
SGSeqhttp://www.bioconductor.org |
| Goldstein, L. D., Cao, Y., Pau, G., Lawrence, M., Wu, T. D., Seshagiri, S., & Gentleman, R. (2016). Prediction and quantification of splice events from RNA-seq data. PloS one, 11(5), e0156132.
| 2016 | |
R package to de novo prediction of splicing events. |
302 |
SpliceJumperhttps://github.com/Reedwarbler/SpliceJumper. |
| Chu, C., Li, X., & Wu, Y. (2015). SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data. BMC bioinformatics, 16, 1-11.
| 2015 | |
a classification-based approach for calling splicing junctions from RNA-seq data. |
303 |
SplicePiehttps://github.com/pulyakhina/splicing_analysis_pipeline |
| Pulyakhina, I., Gazzoli, I., ’t Hoen, P. A., Verwey, N., den Dunnen, J., Aartsma-Rus, A., & Laros, J. F. (2015). SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing. Nucleic acids research, 43(12), e80-e80.
| 2015 | |
SplicePie has three analysis steps: analyzing the order of splicing per sample, looking for recursive splicing events per sample and summarizing predicted recursive splicing events |
304 |
SplicePlothttp://montgomerylab.stanford.edu/splice plot/index.html |
| Wu, E., Nance, T., & Montgomery, S. B. (2014). SplicePlot: a utility for visualizing splicing quantitative trait loci. Bioinformatics, 30(7), 1025-1026.
| 2014 | |
It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files. |
305 |
Vast toolshttps://github.com/vastgroup/vast-tools) |
| Tapial, J., Ha, K. C., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., ... & Irimia, M. (2017). An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome research, 27(10), 1759-1768.
| 2017 | |
A toolset for profiling alternative splicing events in RNA-Seq data |
306 |
TrueSighthttp://bioen-compbio.bioen.illinois.edu/TrueSight/ |
| Li, Y., Li-Byarlay, H., Burns, P., Borodovsky, M., Robinson, G. E., & Ma, J. (2013). TrueSight: a new algorithm for splice junction detection using RNA-seq. Nucleic acids research, 41(4), e51-e51.
| 2013 | |
A Self-training Algorithm for Splice Junction Detection using RNA-seq |
307 |
SwitchSeqhttps://github.com/mgonzalezporta/ SwitchSeq |
| Gonzàlez-Porta, M., & Brazma, A. (2014). Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq. bioRxiv, 005967.
| 2014 | |
set of tools designed to help the users in the interpretation of differential splicing events that affect protein coding genes |
308 |
Portcullishttps://github.com/TGAC/portcullis |
| Mapleson, D., Venturini, L., Kaithakottil, G., & Swarbreck, D. (2018). Efficient and accurate detection of splice junctions from RNA-seq with Portcullis. GigaScience, 7(12), giy131.
| 2018 | |
identification of genuine splice junctions. |
309 |
Rcall toolhttp://mlg.hit.edu.cn/ybai/IR/ IRcallAndIRclass.html |
| Bai, Y., Ji, S., & Wang, Y. (2015, December). IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data. In BMC genomics (Vol. 16, pp. 1-9). BioMed Central.
| 2015 | |
computational tool for IR event detection from RNA-Seq data. |
310 |
IRclassifier toolhttp://mlg.hit.edu.cn/ybai/IR/ IRcallAndIRclass.html |
| Bai, Y., Ji, S., & Wang, Y. (2015, December). IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data. In BMC genomics (Vol. 16, pp. 1-9). BioMed Central.
| 2015 | |
supervised machine learning-based approach for IR event detection from RNA-Seq data. |
311 |
FRASER softwarehttp://bioconductor.org/packages/release/bioc/html/ FRASER.html |
| Mertes, C., Scheller, I. F., Yépez, V. A., Çelik, M. H., Liang, Y., Kremer, L. S., ... & Gagneur, J. (2021). Detection of aberrant splicing events in RNA-seq data using FRASER. Nature communications, 12(1), 529.
| 2021 | |
algorithm to detect aberrant splicing from RNA sequencing data |
312 |
FRASER 2.0 softwarehttps://github.com/gagneurlab/fraser |
| Scheller, I. F., Lutz, K., Mertes, C., Yépez, V. A., & Gagneur, J. (2023). Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index. The American Journal of Human Genetics, 110(12), 2056-2067.
| 2023 | |
advanced algorithms to identify various types of alternative splicing events |
313 |
AIR (Annotation Integrated Resource) toolhttps://panther.appliedbiosystems.com/publications.jsp. |
| Florea, L., Di Francesco, V., Miller, J., Turner, R., Yao, A., Harris, M., ... & Sutton, G. (2005). Gene and alternative splicing annotation with AIR. Genome research, 15(1), 54-66.
| 2005 | |
for predicting genes and their alternatively spliced mRNA transcripts based on genomic alignments of expressed DNA (EST, mRNA) and protein sequences |
314 |
Alamut softwarehttps://www.interactive-biosoftware.com/doc/alamut-visual/2.6/splicing.html |
| Hellen, B. (2009). Splice site tools. A comparative analysis report.
| 2009 | |
developed by Interactive Biosoftware for the interpretation of genetic variants, particularly focusing on their potential effects on splicing |
315 |
JuncBASE (junction based analysis of splicing events)http://compbio.berkeley.edu/proj/juncbase/Home.html |
| Brooks AN, Yang L, Duff MO, et al. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. 2011;21(2):193-202. doi:10.1101/gr.108662.110
| 2011 | |
calculate exon exclusion and inclusion counts to splicing events and to identify statistically significant affected splicing events |
316 |
Matt:Unix toolhttp://matt.crg.eu/ |
| Gohr A, Irimia M. Matt: Unix tools for alternative splicing analysis. Bioinformatics. 2019;35(1):130-132. doi:10.1093/bioinformatics/bty606
| 2019 | |
Unix command-line toolkit for analyzing genomic sequences with focus on the downstream analysis of alternative splicing events |
317 |
MMSplice softwarehttps://github.com/gagneurlab/MMSplice |
| Cheng J, Nguyen TYD, Cygan KJ, et al. MMSplice: modular modeling improves the predictions of genetic variant effects on splicing. Genome Biol. 2019;20(1):48. Published 2019 Mar 1. doi:10.1186/s13059-019-1653-z
| 2019 | |
designed to predict the impact of genetic variants on mRNA splicing. |
318 |
Sircah toolhttp://www.bork.embl.de/Sircah |
| Harrington ED, Bork P. Sircah: a tool for the detection and visualization of alternative transcripts. Bioinformatics. 2008;24(17):1959-1960. doi:10.1093/bioinformatics/btn361
| 2008 | |
detection, analysis and visualization of alternative transcripts |
319 |
Solas softwarehttp://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/ |
| Richard H, Schulz MH, Sultan M, et al. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res. 2010;38(10):e112. doi:10.1093/nar/gkq041
| 2010 | |
means to unravel the intricacies of splicing regulation and its impact on gene expression |
320 |
STAR softwarehttps://github.com/alexdobin/STAR |
| Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635
| 2013 | |
offering unparalleled speed, accuracy, and flexibility in mapping spliced transcripts to the reference genome. |
321 |
Tophat softwarehttps://ccb.jhu.edu/software/tophat/index.shtml |
| Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-1111. doi:10.1093/bioinformatics/btp120
| 2009 | |
efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. |
322 |
UCSC Genome Browser DBhttps://genome.ucsc.edu |
| Navarro Gonzalez J, Zweig AS, Speir ML, et al. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res. 2021;49(D1):D1046-D1057. doi:10.1093/nar/gkaa1070
| 2021 | |
genome browser with annotations on alternative splicing events. |
323 |
rMAPS (RNA Mapping Analysis and Prediction Software)http://rmaps.cecsresearch.org |
| Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y. rMAPS: RNA map analysis and plotting server for alternative exon regulation. Nucleic Acids Res. 2016;44(W1):W333-W338. doi:10.1093/nar/gkw410
| 2016 | |
A tool for the analysis and visualization of alternative splicing events from RNA-Seq data. |
324 |
SpliceRover toolhttp://bioit2.irc.ugent.be/splicerover/ |
| Zuallaert J, Godin F, Kim M, Soete A, Saeys Y, De Neve W. SpliceRover: interpretable convolutional neural networks for improved splice site prediction. Bioinformatics. 2018;34(24):4180-4188. doi:10.1093/bioinformatics/bty497
| 2018 | |
A database of splicing factors and their interactions with RNA transcripts, including alternative splicing regulation. |
325 |
MAJIQ-CAT(Comparative Analysis of Transcriptome) toolhttps://tools.biociphers.org/majiq-cat |
| Aicher JK, Jewell P, Vaquero-Garcia J, Barash Y, Bhoj EJ. Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med. 2020;22(7):1181-1190. doi:10.1038/s41436-020-0780-y
| 2020 | |
A tool for the comparative analysis of alternative splicing events across different conditions or samples. |
326 |
Sashimi Plot softwarehttp://miso.readthedocs.org/en/fastmiso/sashimi.html |
| Katz Y, Wang ET, Silterra J, et al. Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. 2015;31(14):2400-2402. doi:10.1093/bioinformatics/btv034
| 2014 | |
A visualization tool for visualizing read coverage and alternative splicing events from RNA-Seq data. |
327 |
SpliceRack DBhttp://katahdin.cshl.edu:9331/SpliceRack/ |
| Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res. 2006;34(14):3955-3967. doi:10.1093/nar/gkl556
| 2006 | |
A database of alternative splicing events and associated regulatory elements. |
328 |
Whippet toolhttps://github.com/timbitz/Whippet.jl |
| Sterne-Weiler, T., Weatheritt, R. J., Best, A., Ha, K. C., & Blencowe, B. J. (2017). Whippet: an efficient method for the detection and quantification of alternative splicing reveals extensive transcriptomic complexity. bioRxiv, 158519.
| 2017 | |
A tool for the analysis of alternative splicing events and their regulation using RNA-Seq data. |
329 |
MAJIQ-SPEL toolhttp://majiq.biociphers.org/majiq-spel. |
| Green CJ, Gazzara MR, Barash Y. MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data. Bioinformatics. 2018;34(2):300-302. doi:10.1093/bioinformatics/btx565
| 2018 | |
A tool for analyzing and visualizing complex alternative splicing events from RNA-Seq data. |
330 |
SpliceNet toolhttp://www.jjwanglab.org/SpliceNet. |
| Yalamanchili HK, Li Z, Wang P, Wong MP, Yao J, Wang J. SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples. Nucleic Acids Res. 2014;42(15):e121. doi:10.1093/nar/gku577
| 2014 | |
A network-based approach for analyzing alternative splicing events and their regulatory networks |
331 |
FragGeneScan (gene)http://omics.informatics.indiana.edu/FragGeneScan/ |
| Rho M, Tang H, Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38(20):e191. doi:10.1093/nar/gkq747
| 2010 | |
A tool for predicting genes and alternative splicing events from metagenomic sequencing data. |
332 |
SpliceVista tool |
| Zhu Y, Hultin-Rosenberg L, Forshed J, Branca RM, Orre LM, Lehtiö J. SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data. Mol Cell Proteomics. 2014;13(6):1552-1562. doi:10.1074/mcp.M113.031203
| 2014 | |
A web-based tool for interactive visualization of alternative splicing events and their regulatory elements. |
333 |
ASpediaFI DB(https://bioconductor.org/packages/ASpediaFI) |
| Lee K, Yu D, Hyung D, Cho SY, Park C. ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events. Genomics Proteomics Bioinformatics. 2022;20(3):466-482. doi:10.1016/j.gpb.2021.10.004
| 2020 | |
identifying AS events and co-regulated gene interactions implicated in pathways |
334 |
ASCancer Atlas DBhttps://ngdc.cncb.ac.cn/ascancer |
| Wu S, Huang Y, Zhang M, et al. ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers. Nucleic Acids Res. 2023;51(D1):D1196-D1204. doi:10.1093/nar/gkac955
| 2022 | |
implicated in tumor initiation, progression and treatment resistance |
335 |
EASED (Extended Alternatively Spliced EST Database)http://eased.bioinf.mdc-berlin.de/ |
| Lerivray H, Méreau A, Osborne HB. Our favourite alternative splice site. Biol Cell. 2006;98(5):317-321. doi:10.1042/BC20050084
| 2012 | |
Extended Alternatively Spliced EST Database. |
336 |
SpliceNest DBhttp://splicenest.molgen.mpg.de/ |
| Lerivray H, Méreau A, Osborne HB. Our favourite alternative splice site. Biol Cell. 2006;98(5):317-321. doi:10.1042/BC20050084
| 2012 | |
Organism: Human, mouse, Drosophila and Arabidopsis |
337 |
ProSplicer DBhttps://biokeanos.com/source/ProSplicer |
| Lerivray H, Méreau A, Osborne HB. Our favourite alternative splice site. Biol Cell. 2006;98(5):317-321. doi:10.1042/BC20050084
| 2012 | |
The Prosplicer website is of special interest, as it appears to be the only one which also uses protein sequence data |
338 |
EnsEMBL DBhttps://www.ensembl.org |
| Howe KL, Achuthan P, Allen J, et al. Ensembl 2021. Nucleic Acids Res. 2021;49(D1):D884-D891. doi:10.1093/nar/gkaa942
| 2020 | |
annotates genomes and disseminates genomic data for vertebrate species. |
339 |
SpliceVault DBhttps://kidsneuro.shinyapps.io/splicevault/; |
| Dawes R, Bournazos AM, Bryen SJ, et al. SpliceVault predicts the precise nature of variant-associated mis-splicing. Nat Genet. 2023;55(2):324-332. doi:10.1038/s41588-022-01293-8
| 2023 | |
designed to analyze and visualize alternative splicing events across various conditions and tissues |
340 |
SpliceSeq DBhttp://bioinformatics.mdanderson.org/main/SpliceSeq:Overview. |
| Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN. SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts. Bioinformatics. 2012;28(18):2385-2387. doi:10.1093/bioinformatics/bts452
| 2012 | |
a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts |
341 |
AltTrans DBhttp://www.ebi.ac.uk/atd/. |
| Le Texier V, Riethoven JJ, Kumanduri V, et al. AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics. 2006;7:169. Published 2006 Mar 23. doi:10.1186/1471-2105-7-169
| 2006 | |
Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation |
342 |
AspAlt toolN/A |
| Bhasi A, Philip P, Sreedharan VT, Senapathy P. AspAlt: A tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes. Genomics. 2009;94(1):48-54. doi:10.1016/j.ygeno.2009.02.006
| 2009 | |
A tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes |
343 |
HEXEvent DBhttp://hexevent.mmg.uci.edu |
| Busch A, Hertel KJ. HEXEvent: a database of Human EXon splicing Events. Nucleic Acids Res. 2013;41(Database issue):D118-D124. doi:10.1093/nar/gks969
| 2012 | |
a database of Human EXon splicing Events |
344 |
MAPT (gene)https://www.LOVD.nl/MAPT |
| Fischer I. Evolutionary perspective of Big tau structure: 4a exon variants of MAPT. Front Mol Neurosci. 2022;15:1019999. Published 2022 Dec 2. doi:10.3389/fnmol.2022.1019999
| 2022 | |
demonstrate the existence of mature MAPT RNA species that retain intron 3 in human brain samples and to study its correlation with Alzheimer's disease across different regions. |
345 |
MAJIQlopedia DBhttps://majiq.biociphers.org/majiqlopedia/ |
| Quesnel-Vallières M, Jewell S, Lynch KW, Thomas-Tikhonenko A, Barash Y. MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer. Nucleic Acids Res. 2024;52(D1):D213-D221. doi:10.1093/nar/gkad1043
| 2024 | |
an encyclopedia of RNA splicing variations in human tissues and cancer |
346 |
scTEA-dbhttps://www.sctea-db.org/ |
| Barquin M, Kouzel IU, Ehrmann B, Basler M, Gruber AJ. scTEA-db: a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes. Nucleic Acids Res. 2024;52(D1):D1018-D1023. doi:10.1093/nar/gkad878
| 2024 | |
a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes |
347 |
FL-circAS DBhttps://cosbi.ee.ncku.edu.tw/FL-circAS/ |
| Chiang TW, Jhong SE, Chen YC, Chen CY, Wu WS, Chuang TJ. FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing. Nucleic Acids Res. 2024;52(D1):D115-D123. doi:10.1093/nar/gkad829
| 2024 | |
an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing |
348 |
FEICPhttps://github.com/xjyx/FEICP |
| Zhong Y, Yang Y, Wang X, et al. Systematic identification and characterization of exon-intron circRNAs. Genome Res. 2024;34(3):376-393. Published 2024 Apr 25. doi:10.1101/gr.278590.123
| 2024 | |
pipeline for detecting EIciRNAs from HTS data |
349 |
SplicingLore DBhttps://splicinglore.ens-lyon.fr/ |
| Polvèche H, Valat J, Fontrodona N, et al. SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors. Database (Oxford). 2023;2023:baad091. doi:10.1093/database/baad091
| 2023 | |
a web resource for studying the regulation of cassette exons by human splicing factors |
350 |
IDeAS DBDOI: 10.1093/jmcb/mjad074 |
| Zhou H, Yuan L, Ju Y, et al. IDeAS: an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients. J Mol Cell Biol. 2024;15(11):mjad074. doi:10.1093/jmcb/mjad074
| 2023 | |
an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients |
351 |
TGFβ/SNAIL1DOI: 10.1186/s13058-023-01736-y |
| Franco-Valls H, Tusquets-Uxó E, Sala L, et al. Formation of an invasion-permissive matrix requires TGFβ/SNAIL1-regulated alternative splicing of fibronectin. Breast Cancer Res. 2023;25(1):143. Published 2023 Nov 14. doi:10.1186/s13058-023-01736-y
| 2023 | |
Formation of an invasion-permissive matrix requires TGFβ/SNAIL1-regulated alternative splicing of fibronectin |
352 |
DASES DBhttp://www.hxdsjzx.cn/DASES |
| Chen Y, Kuang Y, Luan S, et al. DASES: a database of alternative splicing for esophageal squamous cell carcinoma. Front Genet. 2023;14:1237167. Published 2023 Nov 10. doi:10.3389/fgene.2023.1237167
| 2023 | |
a database of alternative splicing for esophageal squamous cell carcinoma |
353 |
SNORA73BDOI: 10.1111/jcmm.17850 |
| Chen X, Li QH, Xie BM, Ji YM, Han Y, Zhao Y. SNORA73B promotes endometrial cancer progression through targeting MIB1 and regulating host gene RCC1 alternative splicing. J Cell Mol Med. 2023;27(19):2890-2905. doi:10.1111/jcmm.17850
| 2023 | |
promotes endometrial cancer progression through targeting MIB1 and regulating host gene RCC1 alternative splicing |
354 |
SNORD14EDOI: 10.1186/s13046-023-02801-2 |
| Chen X, Liu X, Li QH, et al. A patient-derived organoid-based study identified an ASO targeting SNORD14E for endometrial cancer through reducing aberrant FOXM1 Expression and β-catenin nuclear accumulation. J Exp Clin Cancer Res. 2023;42(1):230. Published 2023 Sep 5. doi:10.1186/s13046-023-02801-2
| 2023 | |
A patient-derived organoid-based study identified an ASO targeting SNORD14E for endometrial cancer through reducing aberrant FOXM1 Expression and β-catenin nuclear accumulation |
355 |
rMATS-turbo Toolhttps://github.com/Xinglab/rmats-turbo |
| Wang Y, Xie Z, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nat Protoc. 2024;19(4):1083-1104. doi:10.1038/s41596-023-00944-2
| 2024 | |
an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data |
356 |
VAST-TOOLShttps://github.com/vastgroup/vast-tools |
| Gohr A, Mantica F, Hermoso-Pulido A, Tapial J, Márquez Y, Irimia M. Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework. Methods Mol Biol. 2022;2537:97-128. doi:10.1007/978-1-0716-2521-7_7
| 2022 | |
help with the biological interpretation of the results, and, ultimately, with the identification of interesting AS events to design wet-lab experiments |
357 |
SWISS-PROT DBhttps://www.expasy.org/resources/uniprotkb-swiss-prot |
| Agosto LM, Gazzara MR, Radens CM, et al. Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome Res. 2019;29(12):2046-2055. doi:10.1101/gr.248435.119
| 2019 | |
matched tandem mass spectra acquired by data-dependent acquisition (DDA) against our custom RNA-seq based database, as well as SWISS-PROT and RefSeq databases to improve identification of splicing-derived proteoforms by 28% compared with use of the SWISS-PROT database alone. |
358 |
RefSeq DBhttps://www.ncbi.nlm.nih.gov/refseq/ |
| Agosto LM, Gazzara MR, Radens CM, et al. Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome Res. 2019;29(12):2046-2055. doi:10.1101/gr.248435.119
| 2019 | |
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration. |
359 |
SpliceDetector softwarehttps://bio.tools/splicedetector |
| Baharlou Houreh M, Ghorbani Kalkhajeh P, Niazi A, Ebrahimi F, Ebrahimie E. SpliceDetector: a software for detection of alternative splicing events in human and model organisms directly from transcript IDs. Sci Rep. 2018;8(1):5063. Published 2018 Mar 22. doi:10.1038/s41598-018-23245-1
| 2018 | |
a software for detection of alternative splicing events in human and model organisms directly from transcript IDs |
360 |
IsoPlot DBhttp://isoplot.iis.sinica.edu.tw/ |
| Ng IM, Huang JH, Tsai SC, Tsai HK. IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes. Database (Oxford). 2017;2017:bax069. doi:10.1093/database/bax069
| 2017 | |
a database for comparison of mRNA isoforms in fruit fly and mosquitoes |
361 |
ASE databaseN/A |
| Zhao L, He S, Liu Z, Song Z, Hou X, Gai L. Bioinformatics analysis of the prognostic role of alternative splicing data in lung adenocarcinoma. J Thorac Dis. 2024;16(2):1463-1472. doi:10.21037/jtd-24-6
| 2023 | |
ASE related to the prognosis of LUAD patients, and provided a theoretical basis for further study of the correlation between ASE and the prognosis of LUAD patients. |
362 |
The Cancer Genome Atlas (TCGA) dbN/A |
| Zhao L, He S, Liu Z, Song Z, Hou X, Gai L. Bioinformatics analysis of the prognostic role of alternative splicing data in lung adenocarcinoma. J Thorac Dis. 2024;16(2):1463-1472. doi:10.21037/jtd-24-6
| 2023 | |
|
363 |
SwissProt dbhttps://www.expasy.org/resources/uniprotkb-swiss-prot |
| Pandi B, Brenman S, Black A, Ng DCM, Lau E, Lam MPY. Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. Preprint. bioRxiv. 2023;2023.10.08.561375. Published 2023 Oct 9. doi:10.1101/2023.10.08.561375
| 2023 | |
Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. |
364 |
betASN/A |
| Ascensão-Ferreira M, Martins-Silva R, Saraiva-Agostinho N, Barbosa-Morais NL. betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions. RNA. 2024;30(4):337-353. Published 2024 Mar 18. doi:10.1261/rna.079764.123
| 2024 | |
intuitive analysis and visualization of differential alternative splicing using beta distributions |
365 |
UALCAN databasehttp://ualcan.path.uab.edu |
| Leng X, Liu J, Jin A, et al. Multi-omics Analyses Reveal Function of Apolipoprotein E in Alternative Splicing and Tumor Immune Microenvironment in Kidney Renal Clear Cell Carcinoma via Pan-cancer Analysis. Cell Biochem Biophys. 2024;82(1):1-13. doi:10.1007/s12013-023-01211-7
| 2024 | |
obtained 73 common APOE genes to perform functional enrichment analysis, assess the correlation between genes and immune cells using TIMER, EPIC, and ssGSEA methods, and examine the prognostic significance using the UALCAN database. |
366 |
STAR softwarehttps://bioinformaticshome.com/tools/rna-seq/descriptions/STAR.html#gsc.tab=0 |
| Tian X, Chen C, Wang X. Sichuan Da Xue Xue Bao Yi Xue Ban. 2023;54(5):874-883. doi:10.12182/20230960501
| 2023 | |
The original sequencing files of the GSE182170 dataset was downloaded from the European Nucleotide Archive (ENA) database with axel, aligned to the reference genome of the ENSEMBL database by using STAR software, and common AS event analysis and visualization were performed with rMATS and rmats2sashimiplot R packages. |
367 |
UCSC Xena databasehttps://docs.ropensci.org/UCSCXenaTools/ |
| Duan C, Zhang Y, Li L, et al. Identification of alternative splicing associated with clinical features: from pan-cancers to genitourinary tumors. Front Oncol. 2023;13:1249932. Published 2023 Sep 25. doi:10.3389/fonc.2023.1249932
| 2023 | |
By analyzing splicing data from the TCGA SpliceSeq database and phenotype data for all TCGA samples from the UCSC Xena database, we identified differential clinical feature-related ASEs in 33 tumors. |
368 |
TIMER2.0 databasehttp://timer.cistrome.org/ |
| Duan C, Zhang Y, Li L, et al. Identification of alternative splicing associated with clinical features: from pan-cancers to genitourinary tumors. Front Oncol. 2023;13:1249932. Published 2023 Sep 25. doi:10.3389/fonc.2023.1249932
| 2023 | |
CIBERSORT immune cell infiltration data from the TIMER2.0 database were used for differential clinical feature-related immune cell infiltration analysis. |
369 |
NSCLC datasetsN/A |
| Han Y, Liu SM, Jin R, Meng W, Wu YL, Li H. A risk score combining co-expression modules related to myeloid cells and alternative splicing associates with response to PD-1/PD-L1 blockade in non-small cell lung cancer. Front Immunol. 2023;14:1178193. Published 2023 Jul 10. doi:10.3389/fimmu.2023.1178193
| 2023 | |
We utilized weighted gene co-expression network analysis (WGCNA) to analyze transcriptomic data from two NSCLC datasets from Gene Expression Omnibus (GSE135222 and GSE126044) that involved patients received ICB treatment. |
370 |
CancerSplicingQTL databasehttps://www.cancersplicingqtl-hust.com/#/ |
| Chen X, Feng J, Zhang Y, et al. MYBL2 alternative splicing-related genetic variants reduce the risk of triple-negative breast cancer in the Chinese population. Front Genet. 2023;14:1150976. Published 2023 Apr 18. doi:10.3389/fgene.2023.1150976
| 2023 | |
The CancerSplicingQTL database and HSF software were used to screen for MYBL2 AS-related genetic variants. |
371 |
HSF softwarehttps://hepsoftwarefoundation.org/ |
| Chen X, Feng J, Zhang Y, et al. MYBL2 alternative splicing-related genetic variants reduce the risk of triple-negative breast cancer in the Chinese population. Front Genet. 2023;14:1150976. Published 2023 Apr 18. doi:10.3389/fgene.2023.1150976
| 2023 | |
The CancerSplicingQTL database and HSF software were used to screen for MYBL2 AS-related genetic variants. |
372 |
MicroExonator DBN/A |
| Fuentes-Beals C, Olivares-Costa M, Andrés ME, et al. Bioinformatic analysis predicts that ethanol exposure during early development causes alternative splicing alterations of genes involved in RNA post-transcriptional regulation. PLoS One. 2023;18(4):e0284357. Published 2023 Apr 13. doi:10.1371/journal.pone.0284357
| 2023 | |
used the bioinformatic tools VAST-TOOLS, rMATS, MAJIQ, and MicroExonator to predict alternative splicing events affected by ethanol from available RNA sequencing data. |
373 |
KEGG analysis Toolhttps://www.genome.jp/kegg/ |
| Fuentes-Beals C, Olivares-Costa M, Andrés ME, et al. Bioinformatic analysis predicts that ethanol exposure during early development causes alternative splicing alterations of genes involved in RNA post-transcriptional regulation. PLoS One. 2023;18(4):e0284357. Published 2023 Apr 13. doi:10.1371/journal.pone.0284357
| 2023 | |
used the bioinformatic tools VAST-TOOLS, rMATS, MAJIQ, and MicroExonator to predict alternative splicing events affected by ethanol from available RNA sequencing data. |
374 |
rmappet pipelinehttps://github.com/didrikolofsson/rmappet/ |
| Olofsson D, Preußner M, Kowar A, Heyd F, Neumann A. One pipeline to predict them all? On the prediction of alternative splicing from RNA-Seq data. Biochem Biophys Res Commun. 2023;653:31-37. doi:10.1016/j.bbrc.2023.02.053
| 2023 | |
we created rmappet, a nextflow pipeline that performs alternative splicing analysis using rMATS and Whippet with subsequent overlapping of the results, enabling robust splicing analysis with only one command |
375 |
AD-gene curated databaseN/A |
| Bhatnagar A, Krick K, Karisetty BC, Armour EM, Heller EA, Elefant F. Tip60's Novel RNA-Binding Function Modulates Alternative Splicing of Pre-mRNA Targets Implicated in Alzheimer's Disease. J Neurosci. 2023;43(13):2398-2423. doi:10.1523/JNEUROSCI.2331-22.2023
| 2023 | |
over half of these altered RNAs are identified as bona-fide Tip60-RNA targets that are enriched for in the AD-gene curated database, with some of these AS alterations prevented against by increasing Tip60 in the fly brain. |
376 |
dCasRxN/A |
| Núñez-Álvarez, Y., Espie--Caullet, T., Buhagiar, G., Rubio-Zulaika, A., Alonso-Marañón, J., Perez-Luna, E., ... & Luco, R. F. (2022). A CRISPR-dCas13 RNA-editing tool to study alternative splicing. bioRxiv, 2022-05.
| 2022 | |
tool to induce specific splice-switching changesin the alternative splicing of endogenous genes |
377 |
GSEA Toolhttps://www.gsea-msigdb.org/gsea/index.jsp |
| Qiao X, Zhu L, Song R, Shang C, Guo Y. CD44 occurring alternative splicing promotes cisplatin resistance and evokes tumor immune response in oral squamous cell carcinoma cells. Transl Oncol. 2023;31:101644. doi:10.1016/j.tranon.2023.101644
| 2023 | |
gene set enrichment analysis. The OSCC Cal27 and HSC4 cisplatin-resistant cell lines were constructed to screen the differential genes/transcripts expression. GO, KEGG and GSEA were performed to reveal the relevant signaling pathways. |
378 |
TIMER toolshttp://cistrome.org/TIMER/ |
| Qiao X, Zhu L, Song R, Shang C, Guo Y. CD44 occurring alternative splicing promotes cisplatin resistance and evokes tumor immune response in oral squamous cell carcinoma cells. Transl Oncol. 2023;31:101644. doi:10.1016/j.tranon.2023.101644
| 2023 | |
R package and TIMER tools were used to evaluate the linear correlation between CD44 and immune cell subpopulations. |
379 |
sequence alignment-based databasehttps://en.vectorbuilder.com/tool/sequence-alignment.html |
| Hao DC, Chen H, Xiao PG, Jiang T. A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales. Curr Genomics. 2022;23(3):207-216. doi:10.2174/1389202923666220527112929
| 2022 | |
When compared with the sequence alignment-based database annotations, DIFFUSE performed better in differentiating isoform functions. |
380 |
DIFFUSE softwarehttps://diffuse.sourceforge.net/ |
| Hao DC, Chen H, Xiao PG, Jiang T. A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales. Curr Genomics. 2022;23(3):207-216. doi:10.2174/1389202923666220527112929
| 2022 | |
The software DIFFUSE was effective in predicting functions of Dichocarpum isoforms, which have not been unearthed. |
381 |
Catsnap dbhttps://catsnap.cesnet.cz/ |
| Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K. Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. New Phytol. 2023;238(4):1722-1732. doi:10.1111/nph.18799
| 2023 | |
a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing |
382 |
CancerSplicing QTL databasehttps://www.cancersplicingqtl-hust.com/#/ |
| He S, Cao R, Mao Y, et al. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk. J Gynecol Oncol. 2023;34(3):e40. doi:10.3802/jgo.2023.34.e40
| 2023 | |
We identified single nucleotide polymorphisms (SNPs) locates in the splicing number trait locus (sQTL) of endometrial cancer using the CancerSplicing QTL database. |
383 |
Kaplan-Meier Plotter dbhttps://kmplot.com/analysis/ |
| He S, Cao R, Mao Y, et al. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk. J Gynecol Oncol. 2023;34(3):e40. doi:10.3802/jgo.2023.34.e40
| 2023 | |
used the Kaplan-Meier Plotter, The Human Protein Atlas, SPNR, and Spliceman2 databases for sQTL and differential gene expression analyses to identify the genetic variant which most potentially influence the risk of endometrial cancer through alternative splicing to reveal the potential mechanism by which candidate SNPs regulate the risk of endometrial cancer. |
384 |
The Human Protein Atlas dbhttps://www.proteinatlas.org/ |
| He S, Cao R, Mao Y, et al. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk. J Gynecol Oncol. 2023;34(3):e40. doi:10.3802/jgo.2023.34.e40
| 2023 | |
we used the Kaplan-Meier Plotter, The Human Protein Atlas, SPNR, and Spliceman2 databases for sQTL and differential gene expression analyses to identify the genetic variant which most potentially influence the risk of endometrial cancer through alternative splicing to reveal the potential mechanism by which candidate SNPs regulate the risk of endometrial cancer. |
385 |
SPNR dbhttps://github.com/SPNR |
| He S, Cao R, Mao Y, et al. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk. J Gynecol Oncol. 2023;34(3):e40. doi:10.3802/jgo.2023.34.e40
| 2023 | |
we used the Kaplan-Meier Plotter, The Human Protein Atlas, SPNR, and Spliceman2 databases for sQTL and differential gene expression analyses to identify the genetic variant which most potentially influence the risk of endometrial cancer through alternative splicing to reveal the potential mechanism by which candidate SNPs regulate the risk of endometrial cancer. |
386 |
Spliceman2 dbhttps://github.com/chsanford/Spliceman-Beta |
| He S, Cao R, Mao Y, et al. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk. J Gynecol Oncol. 2023;34(3):e40. doi:10.3802/jgo.2023.34.e40
| 2023 | |
we used the Kaplan-Meier Plotter, The Human Protein Atlas, SPNR, and Spliceman2 databases for sQTL and differential gene expression analyses to identify the genetic variant which most potentially influence the risk of endometrial cancer through alternative splicing to reveal the potential mechanism by which candidate SNPs regulate the risk of endometrial cancer. |
387 |
ICGC db https://dcc.icgc.org/ |
| Weng Y, Qian H, Hong L, Zhao S, Deng X, Shen B. Identification of EMT-related alternative splicing event of TMC7 to promote invasion and migration of pancreatic cancer. Front Immunol. 2023;13:1089008. Published 2023 Jan 12. doi:10.3389/fimmu.2022.1089008
| 2023 | |
International Cancer Genome Consortium. The EMT-related gene sets, transcriptomes, and matched clinical data were obtained from the MSigDB, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. |
388 |
ssGSEA (gene)https://www.genepattern.org/modules/docs/ssGSEAProjection/4#gsc.tab=0 |
| Yu X, Luo B, Lin J, Zhu Y. Alternative splicing event associated with immunological features in bladder cancer. Front Oncol. 2023;12:966088. Published 2023 Jan 5. doi:10.3389/fonc.2022.966088
| 2023 | |
single-sample gene set enrichment analysis. The single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT algorithm showed that both the risk score model and TRMU were significantly associated with tumor immune microenvironment and immune status (immune cells, immune-related pathway, and immune checkpoint) in BLCA patients. |
389 |
CIBERSORT dbhttps://www.biostars.org/p/428905/ |
| Yu X, Luo B, Lin J, Zhu Y. Alternative splicing event associated with immunological features in bladder cancer. Front Oncol. 2023;12:966088. Published 2023 Jan 5. doi:10.3389/fonc.2022.966088
| 2023 | |
The single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT algorithm showed that both the risk score model and TRMU were significantly associated with tumor immune microenvironment and immune status (immune cells, immune-related pathway, and immune checkpoint) in BLCA patients. |
390 |
STAD dbhttps://bioinformaticstools.org/stad/ |
| Wang X, Huang Z, Li L, et al. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients. Genes (Basel). 2022;14(1):39. Published 2022 Dec 23. doi:10.3390/genes14010039
| 2022 | |
Structural Targets Annotation database |
391 |
CIRCexplorer2 circRNA dbhttps://circexplorer2.readthedocs.io/en/latest/ |
| Das A, Sinha T, Mishra SS, Das D, Panda AC. Identification of potential proteins translated from circular RNA splice variants. Eur J Cell Biol. 2023;102(1):151286. doi:10.1016/j.ejcb.2023.151286
| 2023 | |
we analyzed the previously published HeLa cell RNA-seq datasets to identify circRNA splice variants using the de novo module of the CIRCexplorer2 circRNA annotation pipeline. |
392 |
riboCIRC databaseN/A |
| Das A, Sinha T, Mishra SS, Das D, Panda AC. Identification of potential proteins translated from circular RNA splice variants. Eur J Cell Biol. 2023;102(1):151286. doi:10.1016/j.ejcb.2023.151286
| 2023 | |
several validated circRNAs were predicted to translate into proteins by the riboCIRC database. |
393 |
circCORO1C dbN/A |
| Das A, Sinha T, Mishra SS, Das D, Panda AC. Identification of potential proteins translated from circular RNA splice variants. Eur J Cell Biol. 2023;102(1):151286. doi:10.1016/j.ejcb.2023.151286
| 2023 | |
bioinformatics analysis of proteins derived from splice variants of circCORO1C and circASPH suggested altered protein sequences and structures that could affect their physiological functions. |
394 |
circASPH dbN/A |
| Das A, Sinha T, Mishra SS, Das D, Panda AC. Identification of potential proteins translated from circular RNA splice variants. Eur J Cell Biol. 2023;102(1):151286. doi:10.1016/j.ejcb.2023.151286
| 2023 | |
bioinformatics analysis of proteins derived from splice variants of circCORO1C and circASPH suggested altered protein sequences and structures that could affect their physiological functions. |
395 |
CiteSpace Toolhttps://sourceforge.net/projects/citespace/ |
| Tian B, Bian Y, Bian DJ, et al. Knowledge mapping of alternative splicing of cancer from 2012 to 2021: A bibliometric analysis. Front Oncol. 2022;12:1068805. Published 2022 Dec 14. doi:10.3389/fonc.2022.1068805
| 2022 | |
The Web of Science Core Collection was used to acquire the articles. Utilizing three bibliometric tools (CiteSpace, VOSviewer, R-bibliometrix), we were able to measure and recognize the influence and collaboration data of individual articles, journals, and co-citations. |
396 |
VOSviewer Toolhttps://app.vosviewer.com/ |
| Tian B, Bian Y, Bian DJ, et al. Knowledge mapping of alternative splicing of cancer from 2012 to 2021: A bibliometric analysis. Front Oncol. 2022;12:1068805. Published 2022 Dec 14. doi:10.3389/fonc.2022.1068805
| 2022 | |
The Web of Science Core Collection was used to acquire the articles. Utilizing three bibliometric tools (CiteSpace, VOSviewer, R-bibliometrix), we were able to measure and recognize the influence and collaboration data of individual articles, journals, and co-citations. |
397 |
R-bibliometrix Toolhttps://www.bibliometrix.org/home/index.php/layout/biblioshiny |
| Tian B, Bian Y, Bian DJ, et al. Knowledge mapping of alternative splicing of cancer from 2012 to 2021: A bibliometric analysis. Front Oncol. 2022;12:1068805. Published 2022 Dec 14. doi:10.3389/fonc.2022.1068805
| 2022 | |
The Web of Science Core Collection was used to acquire the articles. Utilizing three bibliometric tools (CiteSpace, VOSviewer, R-bibliometrix), we were able to measure and recognize the influence and collaboration data of individual articles, journals, and co-citations. |
398 |
Spycone Toolhttps://spycone.readthedocs.io/en/latest/ |
| Lio CT, Grabert G, Louadi Z, et al. Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics. 2023;39(1):btac846. doi:10.1093/bioinformatics/btac846
| 2023 | |
Spycone, a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. |
399 |
GDSC databasehttps://www.cancerrxgene.org/ |
| Ma C, Bao Y, Xu J, Xiao B, Li H. Identification and validation of RNA methylation-related alternative splicing gene signature for low-grade glioma to predict survival and immune landscapes. J Cancer Res Clin Oncol. 2023;149(1):47-62. doi:10.1007/s00432-022-04431-1
| 2023 | |
GDSC database to screen potential chemotherapeutic agents. |
400 |
iReckonhttps://ireckonu.com/ |
| Newman JRB, Concannon P, Tardaguila M, Conesa A, McIntyre LM. Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data. G3 (Bethesda). 2018;8(9):2923-2940. Published 2018 Aug 30. doi:10.1534/g3.118.200373
| 2018 | |
We identify 99.8% of true transcripts while iReckon identifies 82% of the true transcripts and creates more transcripts not included in the simulation than were initially used in the simulation. |
401 |
Freddie dbhttps://github.com/vpc-ccg/freddie/ |
| Orabi B, Xie N, McConeghy B, Dong X, Chauve C, Hach F. Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing. Nucleic Acids Res. 2023;51(2):e11. doi:10.1093/nar/gkac1112
| 2023 | |
annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing |
402 |
transcriptomic LR datasetN/A |
| Orabi B, Xie N, McConeghy B, Dong X, Chauve C, Hach F. Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing. Nucleic Acids Res. 2023;51(2):e11. doi:10.1093/nar/gkac1112
| 2023 | |
run Freddie on a transcriptomic LR dataset generated in-house from a prostate cancer cell line with a matched short-read RNA-seq dataset. |
403 |
DEAS DBhttps://www.merriam-webster.com/dictionary/deas |
| Zheng Y, Niu X, Xue W, et al. The Role of Alternative Splicing Factors hnRNP G and Fox-2 in the Progression and Prognosis of Esophageal Cancer. Dis Markers. 2022;2022:3043737. Published 2022 Nov 23. doi:10.1155/2022/3043737
| 2022 | |
Bioinformatics methods were used to further analyzed the differently expressed AS (DEAS) events and their splicing network. |
404 |
Jalview softwarehttps://www.jalview.org/ |
| Pan YJ, Huo FC, Kang MJ, Liu BW, Wu MD, Pei DS. Alternative splicing of HSPA12A pre-RNA by SRSF11 contributes to metastasis potential of colorectal cancer. Clin Transl Med. 2022;12(11):e1113. doi:10.1002/ctm2.1113
| 2022 | |
Jalview software was used to determine the preferential binding motif with relation to exon skipping (ES) events. |
405 |
GEO databasehttps://www.ncbi.nlm.nih.gov/geo/ |
| Zhuo H, Miao S, Jin Z, et al. Metformin Suppresses Hepatocellular Carcinoma through Regulating Alternative Splicing of LGR4. J Oncol. 2022;2022:1774095. Published 2022 Nov 4. doi:10.1155/2022/1774095
| 2022 | |
Gene Expression Omnibus. The GEO database (GSE190076) showed that LGR4 had switching properties in HCC cell lines treated with metformin. |
406 |
ConSpliceMLhttps://github.com/mikecormier/ConSplice |
| Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics. 2022;23(1):482. Published 2022 Nov 14. doi:10.1186/s12859-022-05041-x
| 2022 | |
Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases. |
407 |
MM clinical databasesN/A |
| Zhou Y, Huangfu S, Li M, et al. DAZAP1 facilitates the alternative splicing of KITLG to promote multiple myeloma cell proliferation via ERK signaling pathway. Aging (Albany NY). 2022;14(19):7972-7985. doi:10.18632/aging.204326
| 2022 | |
We first analyzed MM clinical databases and found that MM patients with elevated DAZAP1 had a poor survival. Furthermore, we overexpressed DAZAP1 by lentiviral transfection and utilized siRNA silencing the expression of DAZAP1 in MM cells. DAZAP1 promoted MM cell proliferation in vitro and accelerated MM xenograft tumor growth in vivo. |
408 |
ABLas softwarehttps://github.com/ablifedev/ABLas |
| He C, Zhang G, Lu Y, Zhou J, Ren Z. DDX17 modulates the expression and alternative splicing of genes involved in apoptosis and proliferation in lung adenocarcinoma cells. PeerJ. 2022;10:e13895. Published 2022 Sep 21. doi:10.7717/peerj.13895
| 2022 | |
the DDX17-regulated AS events in A549 cells revealed by computational analysis using ABLas software were strongly validated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR) and were also validated by analysis of The Cancer Genome Atlas (TCGA)-LUAD dataset. |
409 |
(TCGA) LUAD datasethttps://portal.gdc.cancer.gov/projects/TCGA-LUAD |
| He C, Zhang G, Lu Y, Zhou J, Ren Z. DDX17 modulates the expression and alternative splicing of genes involved in apoptosis and proliferation in lung adenocarcinoma cells. PeerJ. 2022;10:e13895. Published 2022 Sep 21. doi:10.7717/peerj.13895
| 2022 | |
the DDX17-regulated AS events in A549 cells revealed by computational analysis using ABLas software were strongly validated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR) and were also validated by analysis of The Cancer Genome Atlas (TCGA)-LUAD dataset. |
410 |
TCGA-HNSCC databasehttps://portal.gdc.cancer.gov/projects/TCGA-HNSC |
| Liu J, Deng W, Xiao Z, Huang X, Lin M, Long Z. Identification of RNA Modification-Associated Alternative Splicing Signature as an Independent Factor in Head and Neck Squamous Cell Carcinoma. J Immunol Res. 2022;2022:8976179. Published 2022 Sep 13. doi:10.1155/2022/8976179
| 2022 | |
AS events and RNA-modified gene expression information were downloaded from TCGA-HNSCC database. |
411 |
RASEs dbhttps://github.com/c2-d2/rase-db-skeleton |
| Yu S, Zhang J, Ding Y, Kang X, Pu X. Genome-wide identification of alternative splicing associated with histone deacetylase inhibitor in cutaneous T-cell lymphomas. Front Genet. 2022;13:937623. Published 2022 Sep 6. doi:10.3389/fgene.2022.937623
| 2022 | |
regulated alternative splicing events. Student's t-tests were performed to evaluate the significance of changes in ratios for AS events, and regulated alternative splicing events (RASEs) were defined as events with p values less than 0.05. The regulatory mechanisms of the RASEs and RBPs were evaluated using Pearson's correlation coefficient. The potential regulatory relationships between RBPs and HDACi-sensitive RASEs were also analyzed. |
412 |
APPRIS databasehttps://appris.bioinfo.cnio.es |
| Pozo F, Rodriguez JM, Martínez Gómez L, Vázquez J, Tress ML. APPRIS principal isoforms and MANE Select transcripts define reference splice variants. Bioinformatics. 2022;38(Suppl_2):ii89-ii94. doi:10.1093/bioinformatics/btac473
| 2022 | |
APPRIS principal isoforms for human, mouse and other model species can be downloaded from the APPRIS database |
413 |
MANE databasehttps://asia.ensembl.org/info/genome/genebuild/mane.html |
| Pozo F, Rodriguez JM, Martínez Gómez L, Vázquez J, Tress ML. APPRIS principal isoforms and MANE Select transcripts define reference splice variants. Bioinformatics. 2022;38(Suppl_2):ii89-ii94. doi:10.1093/bioinformatics/btac473
| 2022 | |
This study compares the longest isoforms, MANE Select transcripts, APPRIS principal isoforms, and expression data, and aims to determine which method is best for selecting biological important reference splice variants for large-scale analyses. |
414 |
GENCODE databasehttps://www.gencodegenes.org/ |
| Pozo F, Rodriguez JM, Martínez Gómez L, Vázquez J, Tress ML. APPRIS principal isoforms and MANE Select transcripts define reference splice variants. Bioinformatics. 2022;38(Suppl_2):ii89-ii94. doi:10.1093/bioinformatics/btac473
| 2022 | |
APPRIS principal isoforms for human, mouse and other model species can be downloaded from the GENCODE genes. |
415 |
FGENESH toolhttp://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind |
| Fatima S, Gupta S, Khan AB, Rehman SU, Jairajpuri MA. Identification and validation of two alternatively spliced novel isoforms of human α-1-antichymotrypsin. Biochem Biophys Res Commun. 2022;628:25-31. doi:10.1016/j.bbrc.2022.08.061
| 2022 | |
scanning of introns, 5' and 3' region of the ACT gene using computational tools like FGENESH and FEX did indicate the presence of coding regions. |
416 |
FEX toolhttp://www.softberry.com/berry.phtml?topic=fex&group=help&subgroup=gfind |
| Fatima S, Gupta S, Khan AB, Rehman SU, Jairajpuri MA. Identification and validation of two alternatively spliced novel isoforms of human α-1-antichymotrypsin. Biochem Biophys Res Commun. 2022;628:25-31. doi:10.1016/j.bbrc.2022.08.061
| 2022 | |
scanning of introns, 5' and 3' region of the ACT gene using computational tools like FGENESH and FEX did indicate the presence of coding regions. |
417 |
ChIP-seq datasethttps://chip-atlas.org/ |
| Wang C, Zong X, Wu F, Leung RWT, Hu Y, Qin J. DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia. Front Mol Biosci. 2022;9:920492. Published 2022 Aug 16. doi:10.3389/fmolb.2022.920492
| 2022 | |
By integrating and analyzing ChIP-seq, CLIP-seq, RNA-seq, and shRNA-seq data in K562 using binding and expression target analysis and Statistical Utility for RBP Functions, we discovered a two-layer regulatory network system centered on these four DRBP-SFs and proposed three possible regulatory models where DRBP-SFs can connect transcriptional and alternative splicing regulatory networks cooperatively in CML. |
418 |
CLIP-seq datasetN/A |
| Wang C, Zong X, Wu F, Leung RWT, Hu Y, Qin J. DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia. Front Mol Biosci. 2022;9:920492. Published 2022 Aug 16. doi:10.3389/fmolb.2022.920492
| 2022 | |
By integrating and analyzing ChIP-seq, CLIP-seq, RNA-seq, and shRNA-seq data in K562 using binding and expression target analysis and Statistical Utility for RBP Functions, we discovered a two-layer regulatory network system centered on these four DRBP-SFs and proposed three possible regulatory models where DRBP-SFs can connect transcriptional and alternative splicing regulatory networks cooperatively in CML. |
419 |
shRNA-seq datasetN/A |
| Wang C, Zong X, Wu F, Leung RWT, Hu Y, Qin J. DNA- and RNA-Binding Proteins Linked Transcriptional Control and Alternative Splicing Together in a Two-Layer Regulatory Network System of Chronic Myeloid Leukemia. Front Mol Biosci. 2022;9:920492. Published 2022 Aug 16. doi:10.3389/fmolb.2022.920492
| 2022 | |
By integrating and analyzing ChIP-seq, CLIP-seq, RNA-seq, and shRNA-seq data in K562 using binding and expression target analysis and Statistical Utility for RBP Functions, we discovered a two-layer regulatory network system centered on these four DRBP-SFs and proposed three possible regulatory models where DRBP-SFs can connect transcriptional and alternative splicing regulatory networks cooperatively in CML. |
420 |
COL3A1N/A |
| Shen Y, Li X, Wang D, et al. COL3A1: Potential prognostic predictor for head and neck cancer based on immune-microenvironment alternative splicing. Cancer Med. 2023;12(4):4882-4894. doi:10.1002/cam4.5170
| 2023 | |
Potential prognostic predictor for head and neck cancer based on immune-microenvironment alternative splicing |
421 |
maser dbhttps://maserdb.net/ |
| Lu Y, Tan L, Xie J, Cheng L, Wang X. Distinct microglia alternative splicing in Alzheimer's disease. Aging (Albany NY). 2022;14(16):6554-6566. doi:10.18632/aging.204223
| 2022 | |
Skipped exon (SE), alternative 3'SS (A3SS), retained intron (RI), alternative 5'SS (A5SS), and mutually exclusive exons (MXE) were evaluated using rMATS and maser. |
422 |
TCGA-BRCA dbhttps://portal.gdc.cancer.gov/projects/TCGA-BRCA |
| Zhang D, Lu W, Zhuo Z, Mei H, Wu X, Cui Y. Construction of a breast cancer prognosis model based on alternative splicing and immune infiltration. Discov Oncol. 2022;13(1):78. Published 2022 Aug 21. doi:10.1007/s12672-022-00506-0
| 2022 | |
A total of 21,232 genes had 45,421 AS events occurring in TCGA-BRCA, while 1604 AS events were found to be significantly correlated with survival. |
423 |
ClinVar databasehttps://www.ncbi.nlm.nih.gov/clinvar/ |
| Gazzaz N, Frost FG, Alderman E, et al. Can tandem alternative splicing and evasion of premature termination codon surveillance contribute to attenuated Peutz-Jeghers syndrome?. Am J Med Genet A. 2022;188(10):3089-3095. doi:10.1002/ajmg.a.62942
| 2022 | |
A review of the ClinVar database identified other similar variants. We suggest that nucleotide changes creating or disrupting tandem alternative splice sites are a pertinent disease mechanism and require contextualization for clinical reporting. |
424 |
ERAD pathwayN/A |
| Lai S, Wang Y, Li T, et al. N6-methyladenosine-mediated CELF2 regulates CD44 alternative splicing affecting tumorigenesis via ERAD pathway in pancreatic cancer. Cell Biosci. 2022;12(1):125. Published 2022 Aug 8. doi:10.1186/s13578-022-00844-0
| 2022 | |
This study indicates that N6-methyladenosine-mediated CELF2 promotes AS of CD44, affecting the ERAD pathway and regulating the biological behavior of PC cells. CELF2 is expected to be a new target for targeted-drug development. |
425 |
ENA databaseshttps://www.ebi.ac.uk/ena/browser/home |
| Lu, Y., Yue, D., Xie, J., Cheng, L., & Wang, X. (2022). Ontology specific alternative splicing changes in Alzheimer’s disease. Frontiers in Genetics, 13, 926049.
| 2022 | |
The GSE132177 dataset was downloaded from GEO and ENA databases, aligned to the GRCm39 reference genome from ENSEMBL via STAR. Alternative 3'SS (A3SS), alternative 5'SS (A5SS), skipped exon (SE), retained intron (RI), and mutually exclusive exons (MXE) AS events were evaluated using rMATS, rmats2sashimiplot, and maser. |
426 |
CPTAC dbN/A |
| Chang, A., Chakiryan, N. H., Du, D., Stewart, P. A., Zhang, Y., Tian, Y., ... & Manley, B. J. (2022). Proteogenomic, epigenetic, and clinical implications of recurrent aberrant splice variants in clear cell renal cell carcinoma. European Urology, 82(4), 354-362.
| 2022 | |
checked for expression across normal tissue in the Genotype-Tissue Expression Project and primary tumor tissue from The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), and our institutional Total Cancer Care database. |
427 |
RBFOX2https://www.genecards.org/cgi-bin/carddisp.pl?gene=RBFOX2 |
| Choi, S., Lee, H. S., Cho, N., Kim, I., Cheon, S., Park, C., ... & Kim, K. K. (2022). RBFOX2-regulated TEAD1 alternative splicing plays a pivotal role in Hippo-YAP signaling. Nucleic Acids Research, 50(15), 8658-8673.
| 2022 | |
regulated TEAD1 alternative splicing plays a pivotal role in Hippo-YAP signaling |
428 |
RBDP dbN/A |
| Thonda, S., Vinnakota, R. L., Kona, S. V., & Kalivendi, S. V. (2022). Identification of RBMX as a splicing regulator in Parkinsonian mimetic induced alternative splicing of α-synuclein. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1865(4), 194825.
| 2022 | |
RNA-Binding Protein Database (RBDP) analysis revealed the presence of four putative RNA binding proteins (RBPs), namely, RBMX, MBNL1, KHDRBS3 and SFRS1 that may bind to the 316 bp region of intron-4and their expression was substantially reduced following MPP+ treatment. |
429 |
LASSO dbhttps://www.enterprisedb.com/docs/lasso/latest/ |
| Chen, J., Liao, Y., Li, R., Luo, M., Wu, G., Tan, R., & Xiao, Z. (2022). Immunotherapeutic Significance of a Prognostic Alternative Splicing Signature in Bladder Cancer. Technology in Cancer Research & Treatment, 21, 15330338221090093.
| 2022 | |
The least absolute shrinkage and selection operator (LASSO) and multivariate Cox analyses were employed to build prognostic signatures. |
430 |
TIME dbN/A |
| Chen, J., Liao, Y., Li, R., Luo, M., Wu, G., Tan, R., & Xiao, Z. (2022). Immunotherapeutic Significance of a Prognostic Alternative Splicing Signature in Bladder Cancer. Technology in Cancer Research & Treatment, 21, 15330338221090093.
| 2022 | |
This study aimed to construct an AS-based prognostic signature and elucidate the role of the tumor immune microenvironment (TIME) and the response to immunotherapy and chemotherapy in bladder cancer. |
431 |
CellMiner databasehttps://discover.nci.nih.gov/cellminer/ |
| Liu, Q., Zhang, H., Yang, X., Liu, X., Yin, F., Guo, P., ... & Han, Y. (2022). Systemic characterization of alternative splicing related to prognosis, immune infiltration, and drug sensitivity analysis in ovarian cancer. Annals of Translational Medicine, 10(2).
| 2022 | |
Relying on drug sensitivity data from the CellMiner database, Genomics of Drug Sensitivity (GDS) was adopted to estimate the platinum-sensitive analysis. |
432 |
ASES toolhttp://www.lcqb.upmc.fr/Ases |
| Zea, D. J., Richard, H., & Laine, E. (2022). ASES: visualizing evolutionary conservation of alternative splicing in proteins. Bioinformatics, 38(9), 2615-2616.
| 2022 | |
visualizing evolutionary conservation of alternative splicing in proteins |
433 |
ONCOMINE DBN/A |
| Zhu, L., Wang, Z., Sun, Y., Giamas, G., Stebbing, J., Yu, Z., & Peng, L. (2021). A prediction model using alternative splicing events and the immune microenvironment signature in lung adenocarcinoma. Frontiers in Oncology, 11, 778637.
| 2021 | |
Gene and protein expression data of Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) were obtained from ONCOMINE and Human Protein Atlas. Splicing factor (SF) regulatory networks were visualized. |
434 |
STRING databasehttps://string-db.org/ |
| Wang, X., Tang, W., Lu, Y., You, J., Han, Y., & Zheng, Y. (2021). Prognostic Significance of Alternative Splicing Genes in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. International Journal of General Medicine, 7933-7949.
| 2021 | |
Functional analysis was operated on Enrichr, STRING database and MCODE analysis were used to evaluate protein-protein interaction (PPI) information. LASSO and multivariate analysis constructed prognostic model and risk analysis of tumor infiltrating immune cells was also conducted. |
435 |
MCODE dbhttps://apps.cytoscape.org/apps/mcode |
| Wang, X., Tang, W., Lu, Y., You, J., Han, Y., & Zheng, Y. (2021). Prognostic Significance of Alternative Splicing Genes in Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma. International Journal of General Medicine, 7933-7949.
| 2021 | |
Functional analysis was operated on Enrichr, STRING database and MCODE analysis were used to evaluate protein-protein interaction (PPI) information. |
436 |
Blast2GO softwarehttps://www.blast2go.com/ |
| Mohammadi, M. A., Harandi, M. F., McManus, D. P., & Mansouri, M. (2021). Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway. Parasites & Vectors, 14, 1-14.
| 2021 | |
Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. |
437 |
X-tile software N/A |
| Chen, B., Deng, T., Deng, L., Yu, H., He, B., Chen, K., ... & Chen, G. (2021). Identification of tumour immune microenvironment-related alternative splicing events for the prognostication of pancreatic adenocarcinoma. BMC cancer, 21, 1-16.
| 2021 | |
The ESTIMATE algorithm was implemented to compute the stromal/immune-related scores of each PAAD patient, followed by Kaplan-Meier (KM) survival analysis of patients with different scores grouped by X-tile software. |
438 |
PASEs dbN/A |
| Xu, W., Anwaier, A., Liu, W., Tian, X., Zhu, W. K., Wang, J., ... & Ye, D. (2021). Systematic genome-wide profiles reveal alternative splicing landscape and implications of splicing regulator DExD-box helicase 21 in aggressive progression of adrenocortical carcinoma. Phenomics, 1, 243-256.
| 2021 | |
Prognosis-related AS events (PASEs) and survival analysis were evaluated based on prediction models constructed by machine-learning algorithm. In total, 23,984 AS events and 3,614 PASEs were detected in the patients with ACC. |
439 |
dbSNP databasehttps://www.ncbi.nlm.nih.gov/snp/ |
| Keegan, N. P., & Fletcher, S. (2022). A spotter’s guide to SNPtic exons: The common splice variants underlying some SNP–phenotype correlations. Molecular Genetics & Genomic Medicine, 10(1), e1840.
| 2022 | |
We thoroughly searched the literature for reported cryptic exons, cross-referenced their genomic coordinates against the dbSNP database of common SNPs, then screened out SNPs with no reported phenotype associations. |
440 |
OMIM NCBI databasehttps://www.ncbi.nlm.nih.gov/omim |
| Trojan, S. E., Dudzik, P., Totoń-Żurańska, J., Laidler, P., & Kocemba-Pilarczyk, K. A. (2021). Expression of alternative splice variants of 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase-4 in normoxic and hypoxic melanoma cells. International Journal of Molecular Sciences, 22(16), 8848.
| 2021 | |
Using RT-qPCR and semi-quantitative RT-PCR, we presented the PFKFB4 gene expression profile at the level of six isoforms described in the OMIM NCBI database in normoxic and hypoxic melanoma cells. |
441 |
VMD softwarehttps://www.ks.uiuc.edu/Research/vmd/ |
| Trojan, S. E., Dudzik, P., Totoń-Żurańska, J., Laidler, P., & Kocemba-Pilarczyk, K. A. (2021). Expression of alternative splice variants of 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase-4 in normoxic and hypoxic melanoma cells. International Journal of Molecular Sciences, 22(16), 8848.
| 2021 | |
using VMD software, we analyzed the structure of isoforms at the protein level, concluding about the catalytic activity of individual isoforms. |
442 |
GO pathwayhttps://geneontology.org/ |
| Liu, J., Mi, C., Long, W., & Sun, T. (2021). Role of alternative splicing events in endometrial cancer prognosis. Zhong nan da xue xue bao. Yi xue ban= Journal of Central South University. Medical Sciences, 46(7), 680-688.
| 2021 | |
Differently expressed AS (DEAS) events were screened by pairing the percent spliced in (PSI) value of tumor and paracancerous tissues in The Cancer Genome Atlas (TCGA) database, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on their parental gene analysis of organisms. |
443 |
ASPNs dbN/A |
| Cheng, R., Xiao, L., Zhou, W., Jin, X., Xu, Z., Xu, C., ... & Jiang, Q. (2021). A pan-cancer analysis of alternative splicing of splicing factors in 6904 patients. Oncogene, 40(35), 5441-5450.
| 2021 | |
developed a splicing-derived neoepitopes database (ASPNs), which provided the corresponding putative alternative splicing-derived neoepitopes of 16 cancer types. |
444 |
RASL-seqhttps://sapac.illumina.com/science/sequencing-method-explorer/kits-and-arrays/rasl-seq.html |
| Oh, J., Pradella, D., Kim, Y., Shao, C., Li, H., Choi, N., ... & Shen, H. (2021). Global alternative splicing defects in human breast cancer cells. Cancers, 13(12), 3071.
| 2021 | |
performed RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq) in breast cancer cells, to identify global breast cancer-specific AS defects. By RT-PCR validation, we demonstrate the high accuracy of RASL-seq results. |
445 |
MS datasethttp://biogps.org/dataset/tag/multiple%20sclerosis/ |
| da Silva, E. M. G., Santos, L. G. C., de Oliveira, F. S., Freitas, F. C. D. P., Parreira, V. D. S. C., Dos Santos, H. G., ... & Passetti, F. (2021). Proteogenomics reveals orthologous alternatively spliced proteoforms in the same human and mouse brain regions with differential abundance in an Alzheimer’s disease mouse model. Cells, 10(7), 1583.
| 2021 | |
Additionally, PKM1 and STXBP1a were detected at higher abundances in a publicly available MS/MS dataset of the AD mouse model APP/PS1 than its wild type. |
446 |
KSCV DBhttps://jiang-lab.shinyapps.io/kscv/ |
| Xiao, L., Zou, G., Cheng, R., Wang, P., Ma, K., Cao, H., ... & Jiang, Q. (2021). Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma. BMC cancer, 21(1), 703.
| 2021 | |
constructed a KIRC-specific stemness prediction model with an AUC of 0.968,and to provide a user-friendly interface of our model for KIRC stemness analysis, we have developed KIRC Stemness Calculator and Visualization (KSCV), hosted on the Shiny server |
447 |
pDESTsplice (vector)https://www.addgene.org/32484/ |
| Putscher, E., Hecker, M., Fitzner, B., Lorenz, P., & Zettl, U. K. (2021). Principles and practical considerations for the analysis of disease-associated alternative splicing events using the gateway cloning-based minigene vectors pDESTsplice and pSpliceExpress. International journal of molecular sciences, 22(10), 5154.
| 2021 | |
The vectors pDESTsplice and pSpliceExpress represent two minigene systems based on Gateway cloning, which are available through the Addgene plasmid repository. we provide an overview of studies in which determinants of alternative splicing were investigated by using pDESTsplice or pSpliceExpress. |
448 |
pSpliceExpress (vector)https://www.addgene.org/32485/ |
| Putscher, E., Hecker, M., Fitzner, B., Lorenz, P., & Zettl, U. K. (2021). Principles and practical considerations for the analysis of disease-associated alternative splicing events using the gateway cloning-based minigene vectors pDESTsplice and pSpliceExpress. International journal of molecular sciences, 22(10), 5154.
| 2021 | |
The vectors pDESTsplice and pSpliceExpress represent two minigene systems based on Gateway cloning, which are available through the Addgene plasmid repository. we provide an overview of studies in which determinants of alternative splicing were investigated by using pDESTsplice or pSpliceExpress. |
449 |
PASA-softwarehttps://github.com/PASApipeline/PASApipeline |
| Wang, Y., Hu, Z., Ye, N., & Yin, H. (2021). IsoSplitter: identification and characterization of alternative splicing sites without a reference genome. RNA, 27(8), 868-875.
| 2021 | |
we evaluated the IsoSplitter pipeline compared with that of the splice junction identification tools, Program to Assemble Spliced Alignments (PASA-software needs a reference genome for AS identification) and AStrap, using data from the model plant Arabidopsis thaliana. |
450 |
AStrap dbN/A |
| Wang, Y., Hu, Z., Ye, N., & Yin, H. (2021). IsoSplitter: identification and characterization of alternative splicing sites without a reference genome. RNA, 27(8), 868-875.
| 2021 | |
IsoSplitter determined more than twice as many AS events than AStrap analysis; and 94.13% of the IsoSplitter predicted AS events were also identified by the PASA analysis. |
451 |
Innate databaseshttps://www.innatedb.com/ |
| Shi, J. Y., Bi, Y. Y., Yu, B. F., Wang, Q. F., Teng, D., & Wu, D. N. (2021). Alternative splicing events in tumor immune infiltration in colorectal cancer. Frontiers in oncology, 11, 583547.
| 2021 | |
analyzed transcriptome profiling and clinical CRC data from The Cancer Genome Atlas (TCGA) database and lists of AS-related and immune-related signatures from the SpliceSeq and Innate databases, respectively to develop and validate a risk model of differential AS events and subsequently a TII risk model. |
452 |
SUPPA2 tool/dbhttps://github.com/comprna/SUPPA |
| Fahmi, N. A., Nassereddeen, H., Chang, J., Park, M., Yeh, H., Sun, J., ... & Zhang, W. (2021). As-quant: Detection and visualization of alternative splicing events with rna-seq data. International journal of molecular sciences, 22(9), 4468.
| 2021 | |
Our extensive experiments on simulated and real datasets demonstrate that AS-Quant outperforms the other three widely used baselines, SUPPA2, rMATS, and diffSplice for detecting alternative splicing events. |
453 |
ce-TopHat toolN/A |
| Pang, T. L., Ding, Z., Liang, S. B., Li, L., Zhang, B., Zhang, Y., ... & Xu, Y. Z. (2021). Comprehensive identification and alternative splicing of microexons in Drosophila. Frontiers in Genetics, 12, 642602.
| 2021 | |
analyzed mRNA-seq data from a variety of Drosophila samples with a newly developed bioinformatic tool, ce-TopHat. In addition to the Flybase annotated, 465 new microexons were identified. |
454 |
GSVA dbN/A |
| Yu, S., Cai, L., Liu, C., Gu, R., Cai, L., & Zhuo, L. (2021). Identification of prognostic alternative splicing events related to the immune microenvironment of hepatocellular carcinoma. Molecular Medicine, 27, 1-15.
| 2021 | |
gene set variation analysis (GSVA) demonstrated that activation of carcinogenic pathways and immune-related pathways in the high-risk group may lead to poor prognosis. |
455 |
Human Protein Atlas databasehttps://www.proteinatlas.org/ |
| Zhang, Y. F., Wang, Y. X., Zhang, N., Lin, Z. H., Wang, L. R., Feng, Y., ... & Wang, L. (2021). Prognostic alternative splicing regulatory network of RBM25 in hepatocellular carcinoma. Bioengineered, 12(1), 1202-1211.
| 2021 | |
The overexpression of CDCA5 and INCENP in HCC patients was examined using the Human Protein Atlas database. |
456 |
Cytoscape softwarehttps://cytoscape.org/ |
| Xu, Q., Xu, H., Deng, R., Li, N., Mu, R., Qi, Z., ... & Huang, W. (2021). Immunological significance of prognostic alternative splicing signature in hepatocellular carcinoma. Cancer cell international, 21, 1-14.
| 2021 | |
Cytoscape software 3.8.0 were employed to visualize AS-splicing factors (SFs) regulatory networks. |
457 |
GCAShttps://gcas.gujgov.edu.in/ |
| Lou, S., Zhang, J., Zhai, Z., Yin, X., Wang, Y., Fang, T., & Xue, Y. (2021). Development and validation of an individual alternative splicing prognostic signature in gastric cancer. Aging (Albany NY), 13(4), 5824.
| 2021 | |
GC-specific AS (GCAS) events were analyzed, and overall survival-associated GCAS (OS-GCAS) events were verified among the genome-wide AS events identified in The Cancer Genome Atlas (TCGA) database. In total, 1,287 GCAS events of 837 genes and 173 OS-GCAS events of 130 genes were identified. |
458 |
RBPDBhttp://rbpdb.ccbr.utoronto.ca/ |
| Louis, J. M., Agarwal, A., Aduri, R., & Talukdar, I. (2021). Global analysis of RNA–protein interactions in TNF‐α induced alternative splicing in metabolic disorders. FEBS letters, 595(4), 476-490.
| 2021 | |
using the database of RNA-binding protein specificities (RBPDB) and our previously published RNA-seq data, we analyzed the interactions between RNA and RNA-binding proteins to decipher the role of alternative splicing in metabolic disorders induced by TNF-α. |
459 |
DRIMSeq toolhttps://bioconductor.org/packages/release/bioc/html/DRIMSeq.html |
| Zorin, E. A., Afonin, A. M., Kulaeva, O. A., Gribchenko, E. S., Shtark, O. Y., & Zhukov, V. A. (2020). Transcriptome analysis of alternative splicing events induced by arbuscular mycorrhizal fungi (Rhizophagus irregularis) in pea (Pisum sativum L.) roots. Plants, 9(12), 1700.
| 2020 | |
Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. |
460 |
IsoformSwitchAnalyzeR toolhttps://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html |
| Zorin, E. A., Afonin, A. M., Kulaeva, O. A., Gribchenko, E. S., Shtark, O. Y., & Zhukov, V. A. (2020). Transcriptome analysis of alternative splicing events induced by arbuscular mycorrhizal fungi (Rhizophagus irregularis) in pea (Pisum sativum L.) roots. Plants, 9(12), 1700.
| 2020 | |
Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. |
461 |
RNA-Seq databaseN/A |
| Zhang, F., Deng, C. K., Wang, M., Deng, B., Barber, R., & Huang, G. (2020). Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq. BMC bioinformatics, 21, 1-17.
| 2020 | |
retrieved high confident, novel alternative splicing biomarkers from the breast cancer RNA-Seq database. |
462 |
Splice-Seq databaseN/A |
| Dong, S., & Lu, L. J. (2020). An alternative splicing signature model for predicting hepatocellular carcinoma-specific survival. Journal of Gastrointestinal Oncology, 11(5), 1054.
| 2020 | |
Data of AS events was obtained from the Splice-Seq database. The corresponding clinical information of HCC was downloaded from The Cancer Genome Atlas (TCGA) data portal. |
463 |
FANTOM5 dbhttps://fantom.gsc.riken.jp/5/ |
| Kajihara, D., Hon, C. C., Abdullah, A. N., Wosniak, J., Moretti, A. I. S., Poloni, J. F., ... & Laurindo, F. R. (2020). Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. Bmc Genomics, 21, 1-16.
| 2020 | |
Extensive analyses using FANTOM5, ENCODE Consortium and GTEx project databases as RNA-seq data sources were performed. |
464 |
ENCODE dbhttps://www.encodeproject.org/ |
| Kajihara, D., Hon, C. C., Abdullah, A. N., Wosniak, J., Moretti, A. I. S., Poloni, J. F., ... & Laurindo, F. R. (2020). Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. Bmc Genomics, 21, 1-16.
| 2020 | |
Extensive analyses using FANTOM5, ENCODE Consortium and GTEx project databases as RNA-seq data sources were performed. |
465 |
Consortium dbN/A |
| Kajihara, D., Hon, C. C., Abdullah, A. N., Wosniak, J., Moretti, A. I. S., Poloni, J. F., ... & Laurindo, F. R. (2020). Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. Bmc Genomics, 21, 1-16.
| 2020 | |
Extensive analyses using FANTOM5, ENCODE Consortium and GTEx project databases as RNA-seq data sources were performed. |
466 |
GTEx dbhttps://gtexportal.org/home/ |
| Kajihara, D., Hon, C. C., Abdullah, A. N., Wosniak, J., Moretti, A. I. S., Poloni, J. F., ... & Laurindo, F. R. (2020). Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. Bmc Genomics, 21, 1-16.
| 2020 | |
Extensive analyses using FANTOM5, ENCODE Consortium and GTEx project databases as RNA-seq data sources were performed. |
467 |
circRNAsN/A |
| Li, X., Zhang, B., Li, F., Yu, K., & Bai, Y. (2020). The mechanism and detection of alternative splicing events in circular RNAs. PeerJ, 8, e10032.
| 2020 | |
Circular RNAs (circRNAs) are considered as functional biomolecules with tissue/development-specific expression patterns. |
468 |
DEGAS DBN/A |
| Qu, Y., Chen, Y., Zhang, L., & Tian, L. (2020). Construction of prognostic predictor by comprehensive analyzing alternative splicing events for colon adenocarcinoma. World Journal of Surgical Oncology, 18, 1-12.
| 2020 | |
differentially expressed genes AS events. A Venn plot analysis was performed between DEGs and prognostic AS events, and the DEGs that co-occurred with prognostic AS events (DEGAS) were identified. |
469 |
PAIRADISE toolhttps://github.com/Xinglab/PAIRADISE |
| Demirdjian, L., Xu, Y., Bahrami-Samani, E., Pan, Y., Stein, S., Xie, Z., ... & Xing, Y. (2020). Detecting allele-specific alternative splicing from population-scale RNA-seq data. The American Journal of Human Genetics, 107(3), 461-472.
| 2020 | |
Paired Replicate Analysis of Allelic Differential Splicing Events (PAIRADISE) provides a useful computational tool for elucidating the genetic variation and phenotypic association of alternative splicing in populations. |
470 |
ASNEO DBhttps://github.com/bm2-lab/ASNEO |
| Zhang, Z., Zhou, C., Tang, L., Gong, Y., Wei, Z., Zhang, G., ... & Yu, J. (2020). ASNEO: identification of personalized alternative splicing based neoantigens with RNA-seq. Aging (Albany NY), 12(14), 14633.
| 2020 | |
Identification of personalized alternative splicing based neoantigens with RNA-seq |
471 |
ESTIMATE dbN/A |
| Hu, C., Wang, Y., Liu, C., Shen, R., Chen, B., Sun, K., ... & Tian, S. (2020). Systematic profiling of alternative splicing for sarcoma patients reveals novel prognostic biomarkers associated with tumor microenvironment and immune cells. Medical Science Monitor: International Medical Journal of Experimental and Clinical Research, 26, e924126-1.
| 2020 | |
we used the CIBERSORT and ESTIMATE package to determine the immune cell proportion and tumor microenvironment (TME) score, respectively. |
472 |
CellProfiler softwarehttps://cellprofiler.org/ |
| Hofmann, L., Kroneis, T., & El-Heliebi, A. (2020). Using in situ padlock probe technology to detect mRNA splice variants in tumor cells. In Situ Hybridization Protocols, 361-378.
| 2020 | |
Quantification can be automated using the image analysis software CellProfiler. |
473 |
Piranha toolN/A |
| Hwang, J. Y., Jung, S., Kook, T. L., Rouchka, E. C., Bok, J., & Park, J. W. (2020). rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Research, 48(W1), W300-W306.
| 2020 | |
rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. |
474 |
PIPE-CLIP toolN/A |
| Hwang, J. Y., Jung, S., Kook, T. L., Rouchka, E. C., Bok, J., & Park, J. W. (2020). rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Research, 48(W1), W300-W306.
| 2020 | |
rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. |
475 |
PARalyzer toolN/A |
| Hwang, J. Y., Jung, S., Kook, T. L., Rouchka, E. C., Bok, J., & Park, J. W. (2020). rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Research, 48(W1), W300-W306.
| 2020 | |
rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. |
476 |
BRCA1 splice variantsN/A |
| Chevalier, L. M., Billaud, A., Fronteau, S., Dauvé, J., Patsouris, A., Verriele, V., & Morel, A. (2020). Somatic mRNA analysis of BRCA1 splice variants provides a direct theranostic impact on PARP inhibitors. Molecular Diagnosis & Therapy, 24, 233-243.
| 2020 | |
Provides a Direct Theranostic Impact on PARP Inhibitors |
477 |
UMD dbhttp://www.umd.be/ |
| Chevalier, L. M., Billaud, A., Fronteau, S., Dauvé, J., Patsouris, A., Verriele, V., & Morel, A. (2020). Somatic mRNA analysis of BRCA1 splice variants provides a direct theranostic impact on PARP inhibitors. Molecular Diagnosis & Therapy, 24, 233-243.
| 2020 | |
Our molecular approach made it possible to visualize the splicing outcomes of three variants (c.5194-2A>G, c.5434C>G, and c.547+1G>A) already identified and present in databases and/or identified with prediction tools (ClinVar, UMD, ARUP Utah database, and Human Splice Finder splices sites prediction) and to confirm their exon skipping consequences, their expression in tumors, and thus their pathogenicity. |
478 |
ARUP Utah dbN/A |
| Chevalier, L. M., Billaud, A., Fronteau, S., Dauvé, J., Patsouris, A., Verriele, V., & Morel, A. (2020). Somatic mRNA analysis of BRCA1 splice variants provides a direct theranostic impact on PARP inhibitors. Molecular Diagnosis & Therapy, 24, 233-243.
| 2020 | |
Our molecular approach made it possible to visualize the splicing outcomes of three variants (c.5194-2A>G, c.5434C>G, and c.547+1G>A) already identified and present in databases and/or identified with prediction tools (ClinVar, UMD, ARUP Utah database, and Human Splice Finder splices sites prediction) and to confirm their exon skipping consequences, their expression in tumors, and thus their pathogenicity. |
479 |
RNA transport pathwayN/A |
| Xie, Z. C., Gao, L., Chen, G., Ma, J., Yang, L. H., He, R. Q., ... & Peng, Z. G. (2020). Prognostic alternative splicing regulatory network of splicing events in acute myeloid leukemia patients based on SpliceSeq data from 136 cases. Neoplasma, 67(3).
| 2020 | |
Enrichment analysis revealed several important genes (TP53, BCL2, AURKB, PPP2R1B, FOS, and BIRC5) and pathways, such as the protein processing pathway in the endoplasmic reticulum, RNA transport pathway, and HTLV-I infection pathway. |
480 |
HTLV-I infection pathwayhttps://www.kegg.jp/pathway/hsa05166 |
| Xie, Z. C., Gao, L., Chen, G., Ma, J., Yang, L. H., He, R. Q., ... & Peng, Z. G. (2020). Prognostic alternative splicing regulatory network of splicing events in acute myeloid leukemia patients based on SpliceSeq data from 136 cases. Neoplasma, 67(3).
| 2020 | |
Enrichment analysis revealed several important genes (TP53, BCL2, AURKB, PPP2R1B, FOS, and BIRC5) and pathways, such as the protein processing pathway in the endoplasmic reticulum, RNA transport pathway, and HTLV-I infection pathway. |
481 |
Embase dbN/A |
| Qi, F., Li, Y., Yang, X., Wu, Y. P., Lin, L. J., & Liu, X. M. (2020). Significance of alternative splicing in cancer cells. Chinese medical journal, 133(02), 221-228.
| 2020 | |
|
482 |
AMPK signaling pathwayhttps://www.cellsignal.com/pathways/ampk-signaling-pathway#:~:text=Pathway%20Description%3A,%2C%20ischemia%2C%20and%20heat%20shock. |
| Zhang, D., Duan, Y., Wang, Z., & Lin, J. (2019). Systematic profiling of a novel prognostic alternative splicing signature in hepatocellular carcinoma. Oncology Reports, 42(6), 2450-2472.
| 2019 | |
A total of 34,163 AS events were detected, among which 1,805 AS events from 1,314 parent genes were significantly associated with the overall survival (OS) of patients with HCC, and their parent genes serve crucial roles in HCC‑related oncogenic processes, including the p53 signaling pathway, AMPK signaling pathway and HIF‑1 signaling pathway. |
483 |
p53 signaling pathwayN/A |
| Zhang, D., Duan, Y., Wang, Z., & Lin, J. (2019). Systematic profiling of a novel prognostic alternative splicing signature in hepatocellular carcinoma. Oncology Reports, 42(6), 2450-2472.
| 2019 | |
A total of 34,163 AS events were detected, among which 1,805 AS events from 1,314 parent genes were significantly associated with the overall survival (OS) of patients with HCC, and their parent genes serve crucial roles in HCC‑related oncogenic processes, including the p53 signaling pathway, AMPK signaling pathway and HIF‑1 signaling pathway. |
484 |
HIF‑1 signaling pathwayhttps://www.cellsignal.com/pathways/hypoxia-signaling-pathway |
| Zhang, D., Duan, Y., Wang, Z., & Lin, J. (2019). Systematic profiling of a novel prognostic alternative splicing signature in hepatocellular carcinoma. Oncology Reports, 42(6), 2450-2472.
| 2019 | |
A total of 34,163 AS events were detected, among which 1,805 AS events from 1,314 parent genes were significantly associated with the overall survival (OS) of patients with HCC, and their parent genes serve crucial roles in HCC‑related oncogenic processes, including the p53 signaling pathway, AMPK signaling pathway and HIF‑1 signaling pathway. |
485 |
IPA toolhttps://github.com/majd/ipatool |
| Louis, J. M., Vaz, C., Balaji, A., Tanavde, V., & Talukdar, I. (2020). TNF-alpha regulates alternative splicing of genes participating in pathways of crucial metabolic syndromes; a transcriptome wide study. Cytokine, 125, 154815.
| 2020 | |
Various bioinformatics tools and databases (for example IPA, KEGG, STRING etc) were used for the pathway and interactome analysis. |
486 |
MIDBhttps://midb.pnb.uconn.edu |
| Olthof, A. M., Hyatt, K. C., & Kanadia, R. N. (2019). Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns. BMC genomics, 20, 1-19.
| 2019 | |
Employed position-weight matrices to obtain a comprehensive updated list of minor introns, consisting of 722 mouse and 770 human minor introns. These can be found in the Minor Intron DataBase (MIDB). |
487 |
Yanagi dbN/A |
| Gunady, M. K., Mount, S. M., & Corrada Bravo, H. (2019). Yanagi: fast and interpretable segment-based alternative splicing and gene expression analysis. BMC bioinformatics, 20, 1-19.
| 2019 | |
Fast and interpretable segment-based alternative splicing and gene expression analysis |
488 |
DSC dbhttps://home.jbnu.ac.kr/NSCL/dsc.htm |
| Louadi, Z., Oubounyt, M., Tayara, H., & Chong, K. T. (2019). Deep splicing code: Classifying alternative splicing events using deep learning. Genes, 10(8), 587.
| 2019 | |
Classifying Alternative Splicing Events Using Deep Learning |
489 |
SMRT dbN/A |
| Ma, J., Xiang, Y., Xiong, Y., Lin, Z., Xue, Y., Mao, M., ... & Huang, Z. (2019). SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus. PeerJ, 7, e7062.
| 2019 | |
single-molecule real-time, reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus |
490 |
public GenBank databasehttp://www.ncbi.nlm.nih.gov/genbank/ |
| Ma, J., Xiang, Y., Xiong, Y., Lin, Z., Xue, Y., Mao, M., ... & Huang, Z. (2019). SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus. PeerJ, 7, e7062.
| 2019 | |
Ananas comosus var. bracteatus is an herbaceous perennial monocot cultivated as an ornamental plant for its chimeric leaves. Because of its genomic complexity, and because no genomic information is available in the public GenBank database |
491 |
NF-kappaB pathwayhttps://www.cellsignal.com/pathways/nfkb-signaling-pathway |
| Zhang, D., Duan, Y., Cun, J., & Yang, Q. (2019). Identification of prognostic alternative splicing signature in breast carcinoma. Frontiers in genetics, 10, 445194.
| 2019 | |
Parent genes of these prognostic events were involved in BRCA-related processes including NF-kappaB and HIF-1 signaling pathway. |
492 |
HIF-1 signaling pathwayhttps://www.cellsignal.com/pathways/hypoxia-signaling-pathway |
| Zhang, D., Duan, Y., Cun, J., & Yang, Q. (2019). Identification of prognostic alternative splicing signature in breast carcinoma. Frontiers in genetics, 10, 445194.
| 2019 | |
Parent genes of these prognostic events were involved in BRCA-related processes including NF-kappaB and HIF-1 signaling pathway. |
493 |
miRNA dbhttps://www.mirbase.org/ |
| Wang, H., Wang, H., Zhang, H., Liu, S., Wang, Y., Gao, Y., ... & Gu, L. (2019). The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species. Bioinformatics, 35(17), 3119-3126.
| 2019 | |
Among them, there were 64 781 and 41 146 miRNA target sites located in linear and circular AS region, respectively. |
494 |
ASmiR dbhttp://forestry.fafu.edu.cn/bioinfor/db/ASmiR |
| Wang, H., Wang, H., Zhang, H., Liu, S., Wang, Y., Gao, Y., ... & Gu, L. (2019). The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species. Bioinformatics, 35(17), 3119-3126.
| 2019 | |
comprehensive database of miRNA targets in alternatively spliced linear and circRNAs (ASmiR) and a web server for deposition and identification of miRNA target sites located in the alternatively spliced region of linear and circular RNAs. |
495 |
psichomics dbhttps://www.bioconductor.org/packages/release/bioc/html/psichomics.html |
| Saraiva-Agostinho, N., & Barbosa-Morais, N. L. (2019). Psichomics: graphical application for alternative splicing quantification and analysis. Nucleic acids research, 47(2), e7-e7.
| 2019 | |
graphical application for alternative splicing quantification and analysis |
496 |
EST dbN/A |
| Krishnaswamy, S., Bukhari, I., Mohammed, A. K., Amer, O. E., Tripathi, G., Alokail, M. S., & Al-Daghri, N. M. (2018). Identification of the splice variants of Recepteur d'Origine nantais (RON) in lung cancer cell lines. Gene, 679, 335-340.
| 2018 | |
Expressed sequence tag (EST) database search indicated that the splicing variant lacking exons 11-13 was a novel one. |
497 |
Matt toolhttps://gitlab.com/aghr/matt |
| Gohr, A., & Irimia, M. (2019). Matt: Unix tools for alternative splicing analysis. Bioinformatics, 35(1), 130-132.
| 2019 | |
Unix tools for alternative splicing analysis |
498 |
SFMetaDBhttp://sfmetadb.ece.tamu.edu |
| Li, J., & Yu, P. (2018). Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis. Scientific Reports, 8(1), 4124.
| 2018 | |
our splicing signature comparison analysis using the psoriasis datasets and our curated splicing factor perturbation RNA-Seq database, SFMetaDB, identified nine candidate splicing factors that may be important in regulating splicing in the psoriasis mouse model dataset. |
499 |
SpliceHunter dbN/A |
| Kuang, Z., & Canzar, S. (2018). Tracking alternatively spliced isoforms from long reads by SpliceHunter. Transcriptome Data Analysis: Methods and Protocols, 73-88.
| 2018 | |
SpliceHunter, a tool for the computational interpretation of long reads generated by for example Pacific Biosciences instruments. SpliceHunter defines and tracks isoforms and novel transcription units across time points, compares their splicing pattern to a reference annotation, and translates them into potential protein sequences. |
500 |
RSEM softwarehttps://github.com/deweylab/RSEM |
| Cardoso, T. F., Quintanilla, R., Castelló, A., González-Prendes, R., Amills, M., & Cánovas, Á. (2018). Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles. BMC genomics, 19, 1-12.
| 2018 | |
using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). |
501 |
DESeq2 softwarehttps://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Cardoso, T. F., Quintanilla, R., Castelló, A., González-Prendes, R., Amills, M., & Cánovas, Á. (2018). Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles. BMC genomics, 19, 1-12.
| 2018 | |
using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). |
502 |
mTOR pathwayN/A |
| Passacantilli, I., Frisone, P., De Paola, E., Fidaleo, M., & Paronetto, M. P. (2017). hnRNPM guides an alternative splicing program in response to inhibition of the PI3K/AKT/mTOR pathway in Ewing sarcoma cells. Nucleic Acids Research, 45(21), 12270-12284.
| 2017 | |
uncover an hnRNPM-dependent alternative splicing program set in motion by inhibition of the mTOR/AKT/PI3K pathway in ES cells that limits therapeutic efficacy of pharmacologic inhibitors, suggesting that combined inhibition of the PI3K/AKT/mTOR pathway and hnRNPM activity may represent a novel approach for ES treatment. |
503 |
p53 databasesN/A |
| Makarov, E. M., Shtam, T. A., Kovalev, R. A., Pantina, R. A., Varfolomeeva, E. Y., & Filatov, M. V. (2017). The rare nonsense mutation in p53 triggers alternative splicing to produce a protein capable of inducing apoptosis. PLoS One, 12(9), e0185126.
| 2016 | |
The mutation eliminates the recognition site for the restriction endonuclease Sca I that allowed us to carry out RFLP analysis of DNA extracted from the clinical samples and suggests that this mutation is more frequent than is documented in the p53 databases. |
504 |
Cuffdiff DBN/A |
| Li, Z., Zhao, K., & Tian, H. (2017). Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing. Oncology letters, 14(2), 1519-1525.
| 2017 | |
The differential expression (DE) and differential alternative splicing (DAS) genes were screened out through Cuffdiff and rMATS, respectively. |
505 |
Manananggal dbN/A |
| Barann, M., Zimmer, R., & Birzele, F. (2017). Manananggal-a novel viewer for alternative splicing events. BMC bioinformatics, 18, 1-13.
| 2017 | |
an application specifically designed for the identification of splicing events in next generation sequencing data. Manananggal is an interactive web application that offers functions specifically tailored to the identification of alternative splicing events that other tools are lacking. |
506 |
SpliVap DBhttp://www.bioinformatica.crs4.org/tools/dbs/splivap/ |
| Floris, M., Orsini, M., & Thanaraj, T. A. (2008). Splice-mediated Variants of Proteins (SpliVaP)–data and characterization of changes in signatures among protein isoforms due to alternative splicing. BMC genomics, 9, 1-23.
| 2008 | |
data and characterization of changes in signatures among protein isoforms due to alternative splicing |
507 |
EMBL – BANK nucleotide sequence databasehttp://www.ebi.ac.uk/embl/ |
| Stoesser, G., Baker, W., van den Broek, A., Camon, E., Garcia-Pastor, M., Kanz, C., ... & Vaughan, R. (2002). The EMBL nucleotide sequence database. Nucleic acids research, 30(1), 21-26.
| 2002 | |
Incorporates , organises , and distributes nucleotide sequences from all available public resources |
508 |
TIGR genehttp://www.tigr.org/tdb/tgi.shtml |
| Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., ... & White, J. (2001). The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Research, 29(1), 159-164.
| 2001 | |
tool for identification ,, categorization of gene sequences |
509 |
Alt Splice dbhttp://proteomics.ysu.edu/altsplice |
| Min, X. J., Powell, B., Braessler, J., Meinken, J., Yu, F., & Sablok, G. (2015). Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops. BMC genomics, 16, 1-13.
| 2015 | |
Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. |
510 |
Splicing factorsN/A |
| Du, J. X., Zhu, G. Q., Cai, J. L., Wang, B., Luo, Y. H., Chen, C., ... & Dai, Z. (2021). Splicing factors: insights into their regulatory network in alternative splicing in cancer. Cancer letters, 501, 83-104.
| 2021 | |
Insights into their regulatory network in alternative splicing in cancer |
511 |
RJunBase DBhttp://www.rjunbase.org/ |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
a database of RNA splice junctions in human normal and cancerous tissues |
512 |
JuncDBhttp://juncdb.carmelab.huji.ac.il/ |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
an exon-exon junction database was established for the comparison of architectures between orthologous transcripts across 88 eukaryotic species |
513 |
intropolis databasehttp://intropolis.rail.bio |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
aligned 21,504 Illumina-sequenced human RNA samples and found 56 861 unannotated novel junctions, which were made available on the intropolis database |
514 |
CSCD databasehttp://gb.whu.edu.cn/CSCD |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
In the scope of human cancers, created the CSCD database to provide a visual interface for exploring the function and regulation of cancer-specific circRNAs based on cancer cell lines. |
515 |
FusionGDB databasehttps://ccsm.uth.edu/FusionGDB |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
the FusionGDB database also offers an integrative resource of gene fusions, including cancer-associated transcript fusions across all cancers |
516 |
BEDToolshttps://bedtools.readthedocs.io/ |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
Linear junctions were matched onto gene coordinates using the genomic intersection functionality of BEDTools and were further classified as intragenic or intergenic junctions. |
517 |
MiOncoCirc databasehttps://mioncocirc.github.io/ |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
The location and expression information of back-splice junctions from over 2000 samples across 27 cancer types were obtained from MiOncoCirc database |
518 |
PrEcise STatistical db (DEEPEST)https://github.com/salzmanlab/DEEPEST-Fusion |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
developed the DataEnriched Efficient PrEcise STatistical (DEEPEST) fusion detection algorithm to detect gene fusions emerging at annotated exon boundaries. |
519 |
MySQL DatabaseN/A |
| Li, Q., Lai, H., Li, Y., Chen, B., Chen, S., Li, Y., ... & Huang, S. (2021). RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. Nucleic Acids Research, 49(D1), D201-D211.
| 2021 | |
All data were handled and organized into a MySQL Database Management System (version 5.7). |
520 |
AtNAGNAG DBN/A |
| Zhang, Q., Zhang, Q., Li, S., Ye, J., Tang, W., Yin, M., ... & Zhang, G. (2018, October). AtNAGNAG: a comprehensive database for NAGNAG alternative splicing in Arabidopsis thaliana. In Proceedings of the 2nd International Conference on Big Data Research (pp. 33-37).
| 2018 | |
a comprehensive database for NAGNAG alternative splicing in Arabidopsis thaliana |
521 |
IRIS dbhttps://github.com/Xinglab/IRIS |
| Pan, Y., Lee, A. H., Yang, H. T., Wang, Y., Xu, Y., Kadash-Edmondson, K. E., ... & Xing, Y. (2019). IRIS: Big data-informed discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. bioRxiv, 843268.
| 2019 | |
Big data-informed discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing |
522 |
ASNP dbDOI: 10.23880/aabsc-16000170 |
| Mao S1, Wen J2, Feng Y3, Zhao W2 and Zhou X2*
| 2021 | |
A Personalized Alternative Splicing Neoantigen Discovery Pipeline |
523 |
JCAST softwarehttps://pypi.org/project/jcast/ |
| | | |
|
524 |
Meet IRIS toolN/A |
| | 2023 | |
The Innovative Computational Tool for Identifying De Novo Cancer Immunotherapy Targets from pre-mRNA Alternative Splicing |
525 |
Alt Event Finder toolN/A |
| Zhou, A., Breese, M. R., Hao, Y., Edenberg, H. J., Li, L., Skaar, T. C., & Liu, Y. (2012). Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. BMC genomics, 13, 1-10.
| 2012 | |
a tool for extracting alternative splicing events from RNA-seq data |
526 |
ISOGO DBhttps://biotecnun.unav.es/app/isogo |
| Ferrer-Bonsoms, J. A., Cassol, I., Fernández-Acín, P., Castilla, C., Carazo, F., & Rubio, A. (2020). ISOGO: Functional annotation of protein-coding splice variants. Scientific reports, 10(1), 1069.
| 2020 | |
Functional annotation of protein-coding splice variants |
527 |
PISE dbhttps://plantintron.com/ |
| Zhang, H., Jia, J., & Zhai, J. (2023). Plant Intron-Splicing Efficiency Database (PISE): exploring splicing of∼ 1,650,000 introns in Arabidopsis, maize, rice, and soybean from∼ 57,000 public RNA-seq libraries. Science China Life Sciences, 66(3), 602-611.
| 2023 | |
exploring splicing of ∼1,650,000 introns in Arabidopsis, maize, rice, and soybean from ∼57,000 public RNA-seq libraries |
528 |
SplAdder TOOLhttp://github.com/ratschlab/spladder |
| Kahles, A., Ong, C. S., Zhong, Y., & Rätsch, G. (2016). SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. Bioinformatics, 32(12), 1840-1847.
| 2023 | |
identification, quantification and testing of alternative splicing events from RNA-Seq data |
529 |
ASpli softwarehttps://bioconductor.org/packages/release/bioc/html/ASpli.html |
| Mancini, E., Rabinovich, A., Iserte, J., Yanovsky, M., & Chernomoretz, A. (2021). ASpli: integrative analysis of splicing landscapes through RNA-Seq assays. Bioinformatics, 37(17), 2609-2616.
| 2021 | |
Annotated and novel AS events |
530 |
NeoSplicehttps://github.com/Benjamin-Vincent-Lab/NeoSplice |
| Chai, S., Smith, C. C., Kochar, T. K., Hunsucker, S. A., Beck, W., Olsen, K. S., ... & Vincent, B. G. (2022). NeoSplice: a bioinformatics method for prediction of splice variant neoantigens. Bioinformatics Advances, 2(1), vbac032.
| 2022 | |
novel computational method for splice variant neoantigen prediction based on (i) prediction of tumor-specific k-mers from RNA-seq data, (ii) alignment of differentially expressed k-mers to the splice graph and (iii) inference of the variant transcript with MHC binding prediction |
531 |
DJExpress DBhttps://github.com/MauerLab/DJExpress |
| Gallego-Paez, L. M., & Mauer, J. (2022). DJExpress: An integrated application for differential splicing analysis and visualization. Frontiers in Bioinformatics, 2, 786898.
| 2022 | |
represents a novel and versatile tool to analyze and explore alternative splicing phenotypes in health and disease. |
532 |
Kassiopeia DBhttp://www.motorprotein.de/kassiopeia. |
| Hatje, K., & Kollmar, M. (2014). Kassiopeia: a database and web application for the analysis of mutually exclusive exomes of eukaryotes. BMC genomics, 15, 1-12.
| 2014 | |
a database and web application for the analysis of mutually exclusive exomes of eukaryotes |
533 |
UTRdbhttp://utrdb.ba.itb.cnr.it/ |
| Grillo, G., Turi, A., Licciulli, F., Mignone, F., Liuni, S., Banfi, S., ... & Pesole, G. (2010). UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic acids research, 38(suppl_1), D75-D80.
| 2010 | |
a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs |
534 |
PEPPI DBhttp://bio.informatics.iupui.edu/peppi |
| Zhou, A., Zhang, F., & Chen, J. Y. (2010, October). PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. In BMC bioinformatics (Vol. 11, pp. 1-13). BioMed Central.
| 2010 | |
a peptidomic database of human protein isoforms for proteomics experiments |
535 |
IIIDBhttp://syslab.nchu.edu.tw/IIIDB |
| Tseng, Y. T., Li, W., Chen, C. H., Zhang, S., Chen, J. J., Zhou, X. J., & Liu, C. C. (2015, December). IIIDB: a database for isoform-isoform interactions and isoform network modules. In BMC genomics (Vol. 16, pp. 1-7). BioMed Central.
| 2015 | |
a database for isoform-isoform interactions and isoform network modules |
536 |
BaRTv1.0 datasethttps://bio.tools/BaRTv1.0 |
| Rapazote-Flores, P., Bayer, M., Milne, L., Mayer, C. D., Fuller, J., Guo, W., ... & Simpson, C. G. (2019). BaRTv1. 0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC genomics, 20, 1-17.
| 2019 | |
an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq |
537 |
Shiny-Seq toolhttps://github.com/schultzelab/Shiny-Seq |
| Sundararajan, Z., Knoll, R., Hombach, P., Becker, M., Schultze, J. L., & Ulas, T. (2019). Shiny-Seq: advanced guided transcriptome analysis. BMC research notes, 12, 1-5.
| 2019 | |
advanced guided transcriptome analysis |
538 |
NetSeekRhttps://github.com/igbb-popescu-lab/NetSeekR |
| Srivastava, H., Ferrell, D., & Popescu, G. V. (2022). NetSeekR: a network analysis pipeline for RNA-Seq time series data. BMC bioinformatics, 23(1), 54.
| 2022 | |
a network analysis pipeline for RNA-Seq time series data |
539 |
ARPIR softwareN/A |
| Spinozzi, G., Tini, V., Adorni, A., Falini, B., & Martelli, M. P. (2020). ARPIR: automatic RNA-Seq pipelines with interactive report. BMC bioinformatics, 21, 1-14.
| 2020 | |
automatic RNA-Seq pipelines with interactive report |
540 |
RNAdetector softwarehttps://rnadetector.atlas.dmi.unict.it/ |
| La Ferlita, A., Alaimo, S., Di Bella, S., Martorana, E., Laliotis, G. I., Bertoni, F., ... & Pulvirenti, A. (2021). RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC bioinformatics, 22(1), 298.
| 2021 | |
a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis |
541 |
Searchlighthttps://github.com/Searchlight2/Searchlight2 |
| Cole, J. J., Faydaci, B. A., McGuinness, D., Shaw, R., Maciewicz, R. A., Robertson, N. A., & Goodyear, C. S. (2021). Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. BMC bioinformatics, 22, 1-21.
| 2021 | |
automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts |
542 |
TCC-GUIhttps://github.com/swsoyee/TCC-GUI |
| Su, W., Sun, J., Shimizu, K., & Kadota, K. (2019). TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data. BMC research notes, 12, 1-6.
| 2019 | |
a Shiny-based application for differential expression analysis of RNA-Seq count data |
543 |
ISOdbN/A |
| Xie, S. Q., Han, Y., Chen, X. Z., Cao, T. Y., Ji, K. K., Zhu, J., ... & Xiao, C. L. (2018). ISOdb: a comprehensive database of full-length isoforms generated by Iso-Seq. International Journal of Genomics, 2018.
| 2018 | |
A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq |
544 |
LSTrAP toolhttps://github.molgen.mpg.de/proost/LSTrAP |
| Proost, S., Krawczyk, A., & Mutwil, M. (2017). LSTrAP: efficiently combining RNA sequencing data into co-expression networks. BMC bioinformatics, 18, 1-9.
| 2017 | |
efficiently combining RNA sequencing data into co-expression networks |
545 |
TrancriptomeReconstructoR dbN/A |
| Ivanov, M., Sandelin, A., & Marquardt, S. (2021). TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. Bmc Bioinformatics, 22, 1-15.
| 2021 | |
data-driven annotation of complex transcriptomes |
546 |
miRge3.0 toolhttps://github.com/mhalushka/miRge3.0 |
| Patil, A. H., & Halushka, M. K. (2021). miRge3. 0: a comprehensive microRNA and tRF sequencing analysis pipeline. NAR genomics and bioinformatics, 3(3), lqab068.
| 2021 | |
a comprehensive microRNA and tRF sequencing analysis pipeline |
547 |
MGcount DBhttps://github.com/hitaandrea/MGcount |
| Hita, A., Brocart, G., Fernandez, A., Rehmsmeier, M., Alemany, A., & Schvartzman, S. (2022). MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. BMC bioinformatics, 23(1), 39.
| 2022 | |
a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts |
548 |
SCRAPN/A |
| Mills, W. T., Eadara, S., Jaffe, A. E., & Meffert, M. K. (2023). SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data. RNA, 29(1), 1-17.
| 2023 | |
a bioinformatic pipeline for the analysis of small chimeric RNA-seq data |
549 |
Kraken toolhttps://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.html |
| Davis, M. P., van Dongen, S., Abreu-Goodger, C., Bartonicek, N., & Enright, A. J. (2013). Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods, 63(1), 41-49.
| 2013 | |
a set of tools for quality control and analysis of high-throughput sequence data |
550 |
SCORE toolhttps://github.com/SiWolf/SCORE |
| Wolf, S. A., Epping, L., Andreotti, S., Reinert, K., & Semmler, T. (2021). SCORE: Smart Consensus Of RNA Expression—a consensus tool for detecting differentially expressed genes in bacteria. Bioinformatics, 37(3), 426-428.
| 2021 | |
Smart Consensus Of RNA Expression-a consensus tool for detecting differentially expressed genes in bacteria |
551 |
FINDER softwarehttps://findersoftware.com/finder/ |
| Banerjee, S., Bhandary, P., Woodhouse, M., Sen, T. Z., Wise, R. P., & Andorf, C. M. (2021). FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC bioinformatics, 22, 1-26.
| 2021 | |
an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences |
552 |
rnaSeqMap toolN/A |
| Leśniewska, A., & Okoniewski, M. J. (2011). rnaSeqMap: a Bioconductor package for RNA sequencing data exploration. BMC bioinformatics, 12, 1-9.
| 2011 | |
a Bioconductor package for RNA sequencing data exploration |
553 |
ISOexpresso DBhttp://wiki.tgilab.org/ISOexpresso/ |
| Yang, I. S., Son, H., Kim, S., & Kim, S. (2016). ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer. BMC genomics, 17, 1-14.
| 2016 | |
a web-based platform for isoform-level expression analysis in human cancer |
554 |
JUICE dbhttp://genoma.unab.cl/juice_system/ |
| Latorre, M., Silva, H., Saba, J., Guziolowski, C., Vizoso, P., Martinez, V., ... & Meisel, L. A. (2006). JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow. Bmc Bioinformatics, 7, 1-11.
| 2006 | |
a data management system that facilitates the analysis of large volumes of information in an EST project workflow |
555 |
Shark softwarehttps://github.com/AlgoLab/shark |
| Denti, L., Pirola, Y., Previtali, M., Ceccato, T., Della Vedova, G., Rizzi, R., & Bonizzoni, P. (2021). Shark: fishing relevant reads in an RNA-Seq sample. Bioinformatics, 37(4), 464-472.
| 2021 | |
fishing relevant reads in an RNA-Seq sample |
556 |
PertOrg 1.0 DBhttp://www.inbirg.com/pertorg/ |
| Zhai, Z., Zhang, X., Zhou, L., Lin, Z., Kuang, N., Li, Q., ... & Pan, J. (2023). PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation. Nucleic Acids Research, 51(D1), D1094-D1101.
| 2023 | |
a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation |
557 |
Gene Expression Nebulas (GEN) DBhttps://ngdc.cncb.ac.cn/gen/ |
| Zhang, Y., Zou, D., Zhu, T., Xu, T., Chen, M., Niu, G., ... & Zhang, Z. (2022). Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. Nucleic Acids Research, 50(D1), D1016-D1024.
| 2022 | |
a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels |
558 |
p53FamTaG DBhttp://www2.ba.itb.cnr.it/p53FamTaG/ |
| Sbisà, E., Catalano, D., Grillo, G., Licciulli, F., Turi, A., Liuni, S., ... & Gisel, A. (2007). p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data. BMC bioinformatics, 8, 1-12.
| 2007 | |
a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data |
559 |
CGKB DBhttp://cowpeagenomics.med.virginia.edu/CGKB/ |
| Chen, X., Laudeman, T. W., Rushton, P. J., Spraggins, T. A., & Timko, M. P. (2007). CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC bioinformatics, 8, 1-9.
| 2007 | |
an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences |
560 |
Cancer DEIso DBhttp://cosbi4.ee.ncku.edu.tw/DEIso/ |
| Yang, T. H., Chiang, Y. H., Shiue, S. C., Lin, P. H., Yang, Y. C., Tu, K. C., ... & Wu, W. S. (2021). Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers. Computational and Structural Biotechnology Journal, 19, 5149-5159.
| 2021 | |
An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers |
561 |
PID dbhttp://biodb.sdau.edu.cn/PID/index.php |
| Gao, Y., Ge, F., Zhang, R., Yin, D., Zhao, Y., Tang, H., ... & Yang, L. (2021). PID: An integrative and comprehensive platform of plant intron. Computational Biology and Chemistry, 93, 107528.
| 2021 | |
An integrative and comprehensive platform of plant intron |
562 |
GEM2Net dbN/A |
| Zaag, R., Tamby, J. P., Guichard, C., Tariq, Z., Rigaill, G., Delannoy, E., ... & Brunaud, V. (2015). GEM2Net: from gene expression modeling to-omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic acids research, 43(D1), D1010-D1017.
| 2015 | |
from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response |
563 |
ShinySyn dbhttps://github.com/obenno/ShinySyn |
| Xiao, Z., & Lam, H. M. (2022). ShinySyn: a Shiny/R application for the interactive visualization and integration of macro-and micro-synteny data. Bioinformatics, 38(18), 4406-4408.
| 2022 | |
a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data |
564 |
CTDquerier dbhttps://github.com/isglobal-brge/CTDquerier |
| Hernandez-Ferrer, C., & Gonzalez, J. R. (2018). CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies. Bioinformatics, 34(18), 3235-3237.
| 2018 | |
a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies |
565 |
Falco dbhttps://github.com/VCCRI/Falco/ |
| Yang, A., Troup, M., Lin, P., & Ho, J. W. (2017). Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud. Bioinformatics, 33(5), 767-769.
| 2017 | |
a quick and flexible single-cell RNA-seq processing framework on the cloud |
566 |
ViReMaShinyhttps://github.com/routhlab/ViReMaShiny |
| Yeung, J., & Routh, A. L. (2022). ViReMaShiny: an interactive application for analysis of viral recombination data. Bioinformatics, 38(18), 4420-4422.
| 2022 | |
an interactive application for analysis of viral recombination data |
567 |
TOBFAC dbhttp://compsysbio.achs.virginia.edu/tobfac/ |
| Rushton, P. J., Bokowiec, M. T., Laudeman, T. W., Brannock, J. F., Chen, X., & Timko, M. P. (2008). TOBFAC: the database of tobacco transcription factors. BMC bioinformatics, 9, 1-7.
| 2008 | |
the database of tobacco transcription factors |
568 |
SynchWeb dbhttps://diamondlightsource.github.io/SynchWeb/ |
| Fisher, S. J., Levik, K. E., Williams, M. A., Ashton, A. W., & McAuley, K. E. (2015). SynchWeb: a modern interface for ISPyB. Journal of Applied Crystallography, 48(3), 927-932.
| 2015 | |
SynchWeb: a modern interface for ISPyB |
569 |
GobyWebhttp://github.com/CampagneLaboratory/gobyweb2-plugins |
| Dorff, K. C., Chambwe, N., Zeno, Z., Simi, M., Shaknovich, R., & Campagne, F. (2013). GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLoS One, 8(7), e69666.
| 2013 | |
simplified management and analysis of gene expression and DNA methylation sequencing data |
570 |
Omics Pipe toolhttp://sulab.scripps.edu/omicspipe |
| Fisch, K. M., Meißner, T., Gioia, L., Ducom, J. C., Carland, T. M., Loguercio, S., & Su, A. I. (2015). Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinformatics, 31(11), 1724-1728.
| 2015 | |
a community-based framework for reproducible multi-omics data analysis |
571 |
RTCGAToolboxhttp://mksamur.github.io/RTCGAToolbox/ |
| Samur, M. K. (2014). RTCGAToolbox: a new tool for exporting TCGA Firehose data. PloS one, 9(9), e106397.
| 2014 | |
a new tool for exporting TCGA Firehose data |
572 |
TCGA Expedition softwarehttps://github.com/TCGAExpedition/tcga-expedition |
| Chandran, U. R., Medvedeva, O. P., Barmada, M. M., Blood, P. D., Chakka, A., Luthra, S., ... & Jacobson, R. S. (2016). TCGA expedition: a data acquisition and management system for TCGA data. PloS one, 11(10), e0165395.
| 2016 | |
A Data Acquisition and Management System for TCGA Data |
573 |
MIRIA toolhttps://mammal.deepomics.org |
| Feng, X., Wang, Z., Li, H., & Li, S. C. (2019). MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals. BMC bioinformatics, 20, 1-5.
| 2019 | |
a webserver for statistical, visual and meta-analysis of RNA editing data in mammals |
574 |
SRT-Server dbhttps://spatialtranscriptomicsanalysis.com/ |
| Yang, S., & Zhou, X. (2024). SRT-Server: powering the analysis of spatial transcriptomic data. Genome Medicine, 16(1), 18.
| 2024 | |
powering the analysis of spatial transcriptomic data |
575 |
GeneCards Version 3N/A |
| Safran, M., Dalah, I., Alexander, J., Rosen, N., Iny Stein, T., Shmoish, M., ... & Lancet, D. (2010). GeneCards Version 3: the human gene integrator. Database, 2010.
| 2010 | |
the human gene integrator |
576 |
Re-fractionN/A |
| Yang, P., Humphrey, S. J., Fazakerley, D. J., Prior, M. J., Yang, G., James, D. E., & Yang, J. Y. H. (2012). Re-fraction: a machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics. Journal of Proteome Research, 11(5), 3035-3045.
| 2012 | |
a machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics |
577 |
Btrimhttp://graphics.med.yale.edu/trim/ |
| Kong, Y. (2011). Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics, 98(2), 152-153.
| 2011 | |
a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies |
578 |
GADhttps://github.com/bio-projects/GAD |
| Yasser, N., & Karam, A. (2020). GAD: a python script for dividing genome annotation files into feature-based files. Interdisciplinary Sciences: Computational Life Sciences, 12(3), 377-381.
| 2020 | |
A Python Script for Dividing Genome Annotation Files into Feature-Based Files |
579 |
aRNApipe toolhttps://github.com/HudsonAlpha/aRNAPipe |
| Alonso, A., Lasseigne, B. N., Williams, K., Nielsen, J., Ramaker, R. C., Hardigan, A. A., ... & Myers, R. M. (2017). aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments. Bioinformatics, 33(11), 1727-1729.
| 2017 | |
a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments |
580 |
TSSAR toolhttp://rna.tbi.univie.ac.at/TSSAR |
| Amman, F., Wolfinger, M. T., Lorenz, R., Hofacker, I. L., Stadler, P. F., & Findeiß, S. (2014). TSSAR: TSS annotation regime for dRNA-seq data. BMC bioinformatics, 15, 1-11.
| 2014 | |
TSS annotation regime for dRNA-seq data |
581 |
CIPRN/A |
| Ekiz, H. A., Conley, C. J., Stephens, W. Z., & O’Connell, R. M. (2020). CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments. BMC bioinformatics, 21, 1-15.
| 2020 | |
a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments |
582 |
ORMAN dbhttp://orman.sf.net |
| Dao, P., Numanagić, I., Lin, Y. Y., Hach, F., Karakoc, E., Donmez, N., ... & Sahinalp, S. C. (2014). ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinformatics, 30(5), 644-651.
| 2014 | |
optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms |
583 |
FastqPuri toolhttps://github.com/jengelmann/FastqPuri |
| Pérez-Rubio, P., Lottaz, C., & Engelmann, J. C. (2019). FastqPuri: high-performance preprocessing of RNA-seq data. BMC bioinformatics, 20, 1-11.
| 2019 | |
high-performance preprocessing of RNA-seq data |
584 |
baerhunterhttps://github.com/irilenia/baerhunter |
| Ozuna, A., Liberto, D., Joyce, R. M., Arnvig, K. B., & Nobeli, I. (2020). baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data. Bioinformatics, 36(3), 966-969.
| 2020 | |
an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data |
585 |
esATAChttps://www.bioconductor.org/packages/release/bioc/html/esATAC.html |
| Wei, Z., Zhang, W., Fang, H., Li, Y., & Wang, X. (2018). esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis. Bioinformatics, 34(15), 2664-2665.
| 2018 | |
an easy-to-use systematic pipeline for ATAC-seq data analysis |
586 |
GDCRNAToolshttps://github.com/Jialab-UCR/GDCRNATools |
| Li, R., Qu, H., Wang, S., Wei, J., Zhang, L., Ma, R., ... & Jia, Z. (2018). GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC. Bioinformatics, 34(14), 2515-2517.
| 2018 | |
an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC |
587 |
Pathview toolhttp://bioconductor.org/packages/release/bioc/html/pathview.html |
| Luo, W., & Brouwer, C. (2013). Pathview: an R/Bioconductor package for pathway-based data integration and visualization. Bioinformatics, 29(14), 1830-1831.
| 2013 | |
an R/Bioconductor package for pathway-based data integration and visualization |
588 |
NEArender toolhttps://cran.r-project.org/web/packages/NEArender/ |
| Jeggari, A., & Alexeyenko, A. (2017). NEArender: an R package for functional interpretation of ‘omics’ data via network enrichment analysis. BMC bioinformatics, 18, 19-28.
| 2017 | |
an R package for functional interpretation of 'omics' data via network enrichment analysis |
589 |
GOexpress softwareN/A |
| Rue-Albrecht, K., McGettigan, P. A., Hernández, B., Nalpas, N. C., Magee, D. A., Parnell, A. C., ... & MacHugh, D. E. (2016). GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. BMC bioinformatics, 17, 1-12.
| 2016 | |
an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data |
590 |
GOSemSim dbhttp://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html |
| Yu, G., Li, F., Qin, Y., Bo, X., Wu, Y., & Wang, S. (2010). GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics, 26(7), 976-978.
| 2010 | |
an R package for measuring semantic similarity among GO terms and gene products |
591 |
SeqFu softwarehttps://telatin.github.io/seqfu2/ |
| Telatin, A., Fariselli, P., & Birolo, G. (2021). SeqFu: a suite of utilities for the robust and reproducible manipulation of sequence files. Bioengineering, 8(5), 59.
| 2021 | |
A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files |
592 |
CIPHER toolN/A |
| Guzman, C., & D’Orso, I. (2017). CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction. BMC bioinformatics, 18, 1-16.
| 2017 | |
a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction |
593 |
SimBA toolhttp://cractools.gforge.inria.fr/softwares/simba/ |
| Audoux, J., Salson, M., Grosset, C. F., Beaumeunier, S., Holder, J. M., Commes, T., & Philippe, N. (2017). SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. BMC bioinformatics, 18, 1-14.
| 2017 | |
A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines |
594 |
svist4get toolhttps://bitbucket.org/artegorov/svist4get/ |
| Egorov, A. A., Sakharova, E. A., Anisimova, A. S., Dmitriev, S. E., Gladyshev, V. N., & Kulakovskiy, I. V. (2019). svist4get: a simple visualization tool for genomic tracks from sequencing experiments. BMC bioinformatics, 20, 1-6.
| 2019 | |
a simple visualization tool for genomic tracks from sequencing experiments |
595 |
ReviewN/A |
| Roy, B., M Haupt, L., & R Griffiths, L. (2013). Alternative splicing (AS) of genes as an approach for generating protein complexity. Current genomics, 14(3), 182-194.
| 2013 | |
Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity |
596 |
cDNA2Genome toolN/A |
| Del Val, C., Glatting, K. H., & Suhai, S. (2003). cDNA2Genome: a tool for mapping and annotating cDNAs. BMC bioinformatics, 4, 1-8.
| 2003 | |
a tool for mapping and annotating cDNAs |
597 |
GeneScissors pipelinehttp://csbio.unc.edu/genescissors/ |
| Zhang, Z., Huang, S., Wang, J., Zhang, X., Pardo Manuel de Villena, F., McMillan, L., & Wang, W. (2013). GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment. Bioinformatics, 29(13), i291-i299.
| 2013 | |
a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment |
598 |
TARGeT pipelineN/A |
| Han, Y., Burnette III, J. M., & Wessler, S. R. (2009). TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic acids research, 37(11), e78-e78.
| 2009 | |
a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences |
599 |
Seqping pipelineN/A |
| Chan, K. L., Rosli, R., Tatarinova, T. V., Hogan, M., Firdaus-Raih, M., & Low, E. T. L. (2017). Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data. BMC bioinformatics, 18, 1-7.
| 2017 | |
gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data |
600 |
TcruziDBhttp://TcruziDB.org |
| Agüero, F., Zheng, W., Weatherly, D. B., Mendes, P., & Kissinger, J. C. (2006). TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi. Nucleic acids research, 34(suppl_1), D428-D431.
| 2006 | |
an integrated, post-genomics community resource for Trypanosoma cruzi |
601 |
piPipes pipelinehttp://bowhan.github.io/piPipes/ |
| Han, B. W., Wang, W., Zamore, P. D., & Weng, Z. (2014). piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome-and CAGE-seq, ChIP-seq and genomic DNA sequencing. Bioinformatics, 31(4), 593-595.
| 2014 | |
a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing |
602 |
VOLTAhttps://github.com/fhaive/VOLTA |
| Pavel, A., Federico, A., Del Giudice, G., Serra, A., & Greco, D. (2021). Volta: adVanced mOLecular neTwork analysis. Bioinformatics, 37(23), 4587-4588.
| 2021 | |
adVanced mOLecular neTwork Analysis |
603 |
Phytest softwarehttps://github.com/phytest-devs/phytest |
| Wirth W, Mutch S, Turnbull R, Duchene S. Phytest: quality control for phylogenetic analyses. Bioinformatics. 2022;38(22):5124-5125. doi:10.1093/bioinformatics/btac664
| 2022 | |
quality control for phylogenetic analyses |
604 |
SPECTRE toolhttps://github.com/maplesond/SPECTRE |
| Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V. SPECTRE: a suite of phylogenetic tools for reticulate evolution. Bioinformatics. 2018;34(6):1056-1057. doi:10.1093/bioinformatics/btx740
| 2018 | |
a suite of phylogenetic tools for reticulate evolution |
605 |
peaks2utr toolhttps://github.com/haessar/peaks2utr |
| Haese-Hill W, Crouch K, Otto TD. peaks2utr: a robust Python tool for the annotation of 3' UTRs. Bioinformatics. 2023;39(3):btad112. doi:10.1093/bioinformatics/btad112
| 2023 | |
a robust Python tool for the annotation of 3' UTRs |
606 |
PTBPsN/A |
| Chen C, Shang A, Gao Y, et al. PTBPs: An immunomodulatory-related prognostic biomarker in pan-cancer. Front Mol Biosci. 2022;9:968458. Published 2022 Aug 23. doi:10.3389/fmolb.2022.968458
| 2022 | |
An immunomodulatory-related prognostic biomarker in pan-cancer |
607 |
NNSplice |
| Tang, R., Prosser, D. O., & Love, D. R. (2016). Evaluation of bioinformatic programmes for the analysis of variants within splice site consensus regions. Advances in Bioinformatics, 2016(1), 5614058.
| 2016 | |
The programmes comprised Human Splice Finder (HSF), Max Entropy Scan (MES), NNSplice, and ASSP. |
608 |
IRFinder dbhttps://github.com/williamritchie/IRFinder |
| Middleton R, Gao D, Thomas A, et al. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol. 2017;18(1):51. Published 2017 Mar 15. doi:10.1186/s13059-017-1184-4
| 2017 | |
assessing the impact of intron retention on mammalian gene expression |
609 |
LeafCutter |
| Li, Y. I., Knowles, D. A., Humphrey, J., Barbeira, A. N., Dickinson, S. P., Im, H. K., & Pritchard, J. K. (2018). Annotation-free quantification of RNA splicing using LeafCutter. Nature genetics, 50(1), 151-158.
| 2018 | |
LeafCutter identifies variable splicing events from short-read RNA-seq data and finds events of high complexity. |
610 |
FineSplicehttps://sourceforge.net/p/finesplice/ |
| Gatto, A., Torroja-Fungairino, C., Mazzarotto, F., Cook, S. A., Barton, P. J., Sanchez-Cabo, F., & Lara-Pezzi, E. (2014). FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions. Nucleic acids research, 42(8), e71-e71.
| 2014 | |
FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. |
611 |
RSW |
| Bai, Y., Hassler, J., Ziyar, A., Li, P., Wright, Z., Menon, R., ... & Sartor, M. A. (2014). Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. PLoS One, 9(7), e100864.
| 2014 | |
RSW pipeline is a practical approach for identifying non-canonical splice junction sites on a genome-wide level. |
612 |
RSRhttp://bioinf1.indstate.edu/RSR |
| Bai, Y., Kinne, J., Donham, B., Jiang, F., Ding, L., Hassler, J. R., & Kaufman, R. J. (2016). Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data. BMC genomics, 17, 107-117.
| 2016 | |
'Read-Split-Run’ (RSR) for detecting genome-wide Ire1α-targeted genes with non-canonical spliced regions at a faster speed. |
613 |
PASTA |
| Tang, S., & Riva, A. (2013). PASTA: splice junction identification from RNA-Sequencing data. BMC bioinformatics, 14, 1-11.
| 2013 | |
PASTA (Patterned Alignments for Splicing and Transcriptome Analysis) is a splice junction detection algorithm specifically designed for RNA-Seq data, relying on a highly accurate alignment strategy and on a combination of heuristic and statistical methods to identify exon-intron junctions with high accuracy. |
614 |
SplicingCompasshttp://www.ichip.de/software/SplicingCompass.html |
| Aschoff, M., Hotz-Wagenblatt, A., Glatting, K. H., Fischer, M., Eils, R., & König, R. (2013). SplicingCompass: differential splicing detection using RNA-seq data. Bioinformatics, 29(9), 1141-1148.
| 2013 | |
differential splicing detection using RNA-seq data |
615 |
NSMAPhttps://sites.google.com/site/nsmapforrnaseq |
| Xia, Z., Wen, J., Chang, C. C., & Zhou, X. (2011). NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq. BMC bioinformatics, 12, 1-13.
| 2011 | |
a method for spliced isoforms identification and quantification from RNA-Seq |
616 |
rSeqDiff |
| Shi, Y., & Jiang, H. (2013). rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test. PloS one, 8(11), e79448.
| 2013 | |
detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test |
617 |
rSeqNPhttp://www-personal.umich.edu/∼jianghui/rseqnp/ |
| Shi, Y., Chinnaiyan, A. M., & Jiang, H. (2015). rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data. Bioinformatics, 31(13), 2222-2224.
| 2015 | |
a non-parametric approach for detecting differential expression and splicing from RNA-Seq data |
618 |
GPSeqhttp://www-rcf.usc.edu/Bliangche/software.html GPSeq. |
| Srivastava S, Chen L. A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res. 2010;38(17):e170. doi:10.1093/nar/gkq670
| 2010 | |
analyze RNA-seq data to estimate gene and exon expression |
619 |
DSGseqhttp://bioinfo.au.tsinghua.edu.cn/software/DSGseq DSGseq |
| Wang W, Qin Z, Feng Z, Wang X, Zhang X. Identifying differentially spliced genes from two groups of RNA-seq samples. Gene. 2013;518(1):164-170. doi:10.1016/j.gene.2012.11.045
| 2013 | |
identify differentially spliced genes between two groups of samples by comparing read counts on all exons |
620 |
GLiMMPS (Generalized Linear Mixed Model Prediction of sQTL)https://codeload.github.com/Xinglab/GLiMMPS/zip/master GLiMMPS |
| Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome Biol. 2013;14(7):R74. Published 2013 Jul 22. doi:10.1186/gb-2013-14-7-r74
| 2013 | |
statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data |
621 |
RegRNAhttp://regrna.mbc.nctu.edu.tw/ html/prediction.html |
| Huang HY, Chien CH, Jen KH, Huang HD. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006;34(Web Server issue):W429-W434. doi:10.1093/nar/gkl333
| 2006 | |
Identify the homologs of regulatory RNA motifs and elements against an input mRNA sequence. |
622 |
Maxentscanhttp://genes.mit.edu/burgelab/ maxent/Xmaxent.html http://genes.mit.edu/burgelab/ maxent/Xmaxentscan_scoreseq. html http://genes.mit.edu/burgelab/ maxent/ Xmaxentscan_scoreseq_acc. html |
| Yeo, G. W. (2004). Identification, improved modeling and integration of signals to predict constitutive and altering splicing (Doctoral dissertation, Massachusetts Institute of Technology).
| 2004 | |
predicts splice sites in genomic sequences using a maximum entropy model to evaluate their likelihood |
623 |
ERANGE |
| Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods, 5(7), 621-628.
| 2008 | |
The functions of ERANGE are to assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (‘multireads’), assign them to their most likely site(s) of origin |
624 |
rDiff-paramhttp://bioweb.me/rdiff |
| Drewe, P., Stegle, O., Hartmann, L., Kahles, A., Bohnert, R., Wachter, A., ... & Rätsch, G. (2013). Accurate detection of differential RNA processing. Nucleic acids research, 41(10), 5189-5198.
| 2013 | |
|
625 |
PRAP db |
| | | |
|
626 |
APA scan |
| | | |
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