Categories of resources

• Post-analysis categorization
  • Literature search
• Post-survey categorization
  • Features validated in most cases
    • Gene expression
    • MicroRNA
    • Pathways
    • Primer designing
    • Protein-protein interactions (commonly used resources)
    • Protein structure prediction
    • SNP analysis
  • Features not validated
    • Alternative splice form analysis
    • DNA motif detection
    • Microbiology
    • Multiple sequence alignment
    • Next generation sequencing
• Simple lists
  • Carbohydrates
  • Gene ID conversion
  • Lipids
  • Long non-coding RNA
  • piRNA
  • Promoter prediction
  • Protein-protein interactions (all resources)
  • RNA structure prediction
  • SNP
  • SNP analysis
• Preliminary lists
  • Antibodies
  • Biomarkers
  • Cell lines
  • Clinical trials
  • DNA/RNA structures
  • Disease-gene relationships
  • Enzymes
  • Functional analysis
  • Gene Ontology specific analysis
  • Gene/protein unified information
  • Genetics
  • Genomes and Genomics
  • Mass spectrometry
  • Microarray data analysis
  • Molecular docking
  • Nomenclature
  • Organelles
  • Orthologs
  • Pharmacokinetics and Pharmacodynamics
  • Phylogeny/Taxonomy
  • Protein domains
  • Protein localization
  • Protein-nucleic acid interactions
  • Secretome
  • Small molecules
  • Spectral analysis
  • Text-mining
  • Toxicology
  • Transcription factors and binding sites

• Intuitive browsing
• Multi-level categories
• Alphabetical list

1	ACEScan http://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	AceView http://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 Algorithm http://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	Agene http://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 Sequencing http://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	ApiESTDB http://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 Database http://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 Prediction http://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 Genes http://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 Archives http://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	Augustus http://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 Project http://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 Finder http://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 tool http://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-It http://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 EST http://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	ChimerDB http://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 Transcripts http://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 server http://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 Disorder http://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	ESEfinder http://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'Hom http://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-SKIP http://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 miner http://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	ExtraTrain http://www.era7.com/ExtraTrain/index.cfm		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 Database http://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 Database http://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 Finder http://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 Database http://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 Pipeline http://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 Explorer http://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	GeneBuilder http://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	GeneCards http://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	GeneMark http://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	GeneNest http://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	GeneSeqer http://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	Genie http://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	GenomeScan http://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	GenomeThreader http://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	GENSCAN http://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 2 http://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 ER http://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 Databse http://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 Locator http://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	HMMGene http://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-SKIP http://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 Dataset http://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 Finder http://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 Service http://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	Intronerator http://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 Database http://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	MGAlignIt http://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 Finder http://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 Server http://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 2011 http://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 Finder http://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/Silencers http://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 Sequencing http://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 2 http://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 Encyclopedia http://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 Exons http://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-ESE http://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 Database http://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	Scipio http://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	sgp2 http://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	Softberry http://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	Spidey http://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	SpliceIT http://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	SplicePredictor http://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	SpliceScan http://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	SpliceView http://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 Engine http://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 Database http://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	WormBase http://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:Map http://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	SpliceInfo http://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	ProSplicer http://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	ASD http://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	ASD http://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 II http://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	LivestockExp https://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	DEXSeq https://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	DARTS https://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	Pangolin https://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	SpliceAI https://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	ECgene http://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	ECgene http://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-DBAS http://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	HOLLYWOOD http://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	MetazExp https://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	MAJIQlopedia https://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	GTDrift https://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	ASPicDB http://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	ASPIC http://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-CMC https://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	SpliceWiz https://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 2 http://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	TeaAS http://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	CuAS http://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	ASlive ASlive.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	FishExp https://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 SpliceSeq http://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	PlantExp https://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 Omnibus https://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	ASpedia http://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	CASA http://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 db http://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	AVATAR http://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	EuSplice http://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	FungiExp https://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	OncoSplicing www.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	SASD t 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	ASMD http://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	PlantSPEAD http://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	DIGGER https://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-R https://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	CanIsoNet https://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	APPRIS http://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	AsMamDB http://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	CancerSplicingQTL http://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	ExonSkipDB https://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 2 http://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-F http://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	SpliceAid http://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 database http://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	DBASS https://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	EDAS http://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	HYBRIDdb http://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	SpliceMiner http://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	STEPs http://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	ssSNPTarget http://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	PlaASDB http://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	TSVdb http://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	IsoVis https://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	VastDB http://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	dbSNP http://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 DB http://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	HExDB http://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	HASDB http://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	MutSpliceDB https://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	DBATE http://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	MIsoMine http://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	ASDB http://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	GRSDB http://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_DB http://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	ASHESdb http://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	DBASS5 http://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	DBASS3 http://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	SpliceProt http://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	EXPANSION https://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	DEDB http://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	ASHESdb http://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	TCOF1 www.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 Database http://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	Xpro http://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	SEDB http://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	ASTool http://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	MkcDBGAS http://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	SpliceMachine http://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	QPALMA http://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	SplitSeek http://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	SOAPsplice http://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	findAS https://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	SUPPA https://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	PULSE http://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	NAGNAG https://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	SplicingTypesAnno https://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	AltAnalyze http://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	DomainGraph http://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	VALERIE https://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-Scoop https://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	SpliceCenter http://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	PASS https://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	ASimulatoR https://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	ESGq https://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	PathwaySplice https://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	SpliceDetector https://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	DIEGO www.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	jSplice http://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 Express http://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	rMAT rnaseq-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	PrimerSeq http://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	AVISPA http://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	ExonSuite https://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	ASFinder http://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	PIntron http://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	SpliceGrapher https://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	SplicingViewer http://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	HMMSplicer http://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	ISIS http://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	IsoEM http://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	MAISTAS http://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	SpliceTools https://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	SPLOOCE http://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	ASTK https://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	BIPASS http://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	ExInt http://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	EID http://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	NetUTR http://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	HYBRIDdb http://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	IntSplice https://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	IsoFunc https://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	NetGene2 http://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	Spliceport http://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 DB http://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	SimSpliceEvol https://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	MARVEL 10.1093/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	ASmodeler http://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	ASePCR http://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	ASGS http://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	Splicy http://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	AsiDesigner http://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	ExoPLOT http://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	IsoSplitter https://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 Tool https://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	MntJULiP https://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-seq https://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	RNfuzzyApp https://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	rMAPS2 http://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	MapSplice http://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	ExonImpact http://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	DiffSplice http://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	MATS http://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	SpliceTrap http://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-seq http://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	TAPAS http://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	spliceR http://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	ASSP http://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	WebScipio http://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-v2 http://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	PASSion https://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	CLASS2 http://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	Diceseq http://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	Eoulsan http://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	LEMONS http://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-RNA http://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	RSVP http://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	SGSeq http://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	SpliceJumper https://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	SplicePie https://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	SplicePlot http://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 tools https://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	TrueSight http://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	SwitchSeq https://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	Portcullis https://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 tool http://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 tool http://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 software http://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 software https://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) tool https://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 software https://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 tool http://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 software https://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 tool http://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 software http://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 software https://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 software https://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 DB https://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 tool http://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) tool https://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 software http://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 DB http://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 tool https://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 tool http://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 tool http://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 DB https://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 DB http://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 DB https://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 DB https://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 DB https://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 DB http://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 DB http://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 tool N/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 DB http://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 DB https://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-db https://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 DB https://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	FEICP https://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 DB https://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 DB DOI: 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/SNAIL1 DOI: 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 DB http://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	SNORA73B DOI: 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	SNORD14E DOI: 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 Tool https://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-TOOLS https://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 DB https://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 DB https://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 software https://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 DB http://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 database N/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) db N/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 db https://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	betAS N/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 database http://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 software https://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 database https://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 database http://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 datasets N/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 database https://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 software https://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 DB N/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 Tool https://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 pipeline https://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 database N/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	dCasRx N/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 Tool https://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 tools http://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 database https://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 software https://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 db https://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 database https://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 db https://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 db https://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 db https://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 db https://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 db https://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 db https://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 db https://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 database N/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 db N/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 db N/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 Tool https://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 Tool https://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 Tool https://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 Tool https://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 database https://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	iReckon https://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 db https://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 dataset N/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 DB https://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 software https://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 database https://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	ConSpliceML https://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 databases N/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 software https://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 dataset https://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 database https://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 db https://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 database https://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 database https://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 database https://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 tool http://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 tool http://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 dataset https://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 dataset N/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 dataset N/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	COL3A1 N/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 db https://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 db https://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 database https://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 pathway N/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 databases https://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 db N/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	RBFOX2 https://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 db N/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 db https://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 db N/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 database https://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 tool http://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 DB N/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 database https://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 db https://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 software https://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 db N/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 database https://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 database https://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 software https://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 pathway https://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 db N/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-seq https://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 dataset http://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 DB https://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-software https://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 db N/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 databases https://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/db https://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 tool N/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 db N/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 database https://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 software https://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	GCAS https://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	RBPDB http://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 tool https://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 tool https://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 database N/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 database N/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 db https://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 db https://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 db N/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 db https://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	circRNAs N/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 DB N/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 tool https://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 DB https://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 db N/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 software https://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 tool N/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 tool N/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 tool N/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 variants N/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 db http://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 db N/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 pathway N/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 pathway https://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 db N/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 pathway https://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 pathway N/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 pathway https://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 tool https://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	MIDB https://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 db N/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 db https://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 db N/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 database http://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 pathway https://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 pathway https://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 db https://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 db http://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 db https://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 db N/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 tool https://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	SFMetaDB http://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 db N/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 software https://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 software https://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 pathway N/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 databases N/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 DB N/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 db N/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 DB http://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 database http://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 gene http://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 db http://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 factors N/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 DB http://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	JuncDB http://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 database http://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 database http://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 database https://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	BEDTools https://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 database https://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 Database N/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 DB N/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 db https://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 db DOI: 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 software https://pypi.org/project/jcast/		N/A
524	Meet IRIS tool N/A		Banhita Maitra	2023		The Innovative Computational Tool for Identifying De Novo Cancer Immunotherapy Targets from pre-mRNA Alternative Splicing
525	Alt Event Finder tool N/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 DB https://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 db https://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 TOOL http://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 software https://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	NeoSplice https://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 DB https://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 DB http://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	UTRdb http://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 DB http://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	IIIDB http://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 dataset https://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 tool https://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	NetSeekR https://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 software N/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 software https://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	Searchlight https://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-GUI https://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	ISOdb N/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 tool https://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 db N/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 tool https://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 DB https://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	SCRAP N/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 tool https://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 tool https://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 software https://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 tool N/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 DB http://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 db http://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 software https://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 DB http://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) DB https://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 DB http://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 DB http://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 DB http://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 db http://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 db N/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 db https://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 db https://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 db https://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	ViReMaShiny https://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 db http://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 db https://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	GobyWeb http://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 tool http://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	RTCGAToolbox http://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 software https://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 tool https://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 db https://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 3 N/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-fraction N/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	Btrim http://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	GAD https://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 tool https://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 tool http://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	CIPR N/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 db http://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 tool https://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	baerhunter https://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	esATAC https://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	GDCRNATools https://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 tool http://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 tool https://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 software N/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 db http://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 software https://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 tool N/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 tool http://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 tool https://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	Review N/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 tool N/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 pipeline http://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 pipeline N/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 pipeline N/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	TcruziDB http://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 pipeline http://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	VOLTA https://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 software https://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 tool https://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 tool https://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	PTBPs N/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 db https://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	FineSplice https://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	RSR http://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	SplicingCompass http://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	NSMAP https://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	rSeqNP http://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	GPSeq http://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	DSGseq http://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	RegRNA http://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	Maxentscan http://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-param http://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		n/a
626	APA scan		n/a