Alternative splice form analysis

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 Jul 1;34(Web Server issue):W435-9. PubMed PMID: 16845043; PubMed Central PMCID: PMC1538822.

2006

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.
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.

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:S12.1-14. Epub 2006 Aug 7. PubMed PMID: 16925834; PubMed Central PMCID: PMC1810549.

2006

100

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.
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.

Agene
http://servers.binf.ku.dk/agene/

Munch K, Krogh A. Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics. 2006 May 21;7:263. PubMed PMID: 16712739; PubMed Central PMCID: PMC1522026.

2006

100

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/.
"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/."

AS-ALPS - Alternative Splicing Induced Alteration of Protein Structure
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 Jan;37(Database issue):D305-9. Epub 2008 Nov 10. PubMed PMID: 19015123; PubMed Central PMCID: PMC2686549.

2009

100

1) Alternative Splicing type and position is given. 2) Uninformative transcripts can also be seen. 3) Splice site details include the position of the Alternative spliced region.
1) Alternative Splicing type and position is given. 2) Uninformative transcripts can also be seen. 3) Splice site details include the position of the Alternative spliced region.

ASIP - Alternative Splicing in Plants
http://www.plantgdb.org/ASIP/tools/

Search against Arabidopsis and rice introns/exons/exon junctions.

Not available

100

Gene information includes start and end position, chromosome number.
Gene information includes start and end position, chromosome number.

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. Epub 2004 Nov 29. PubMed PMID: 15575968; PubMed Central PMCID:PMC545797.

2004

100

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.
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.

ASTRA - Alternative Splicing and TRanscription Archives
http://alterna.cbrc.jp/

Database for identification of patterns of alternative splicing and transcriptional initiation. Exons introns structures of splice variants can be viewed on java applet.

Not available

100

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.
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.

GeneBuilder
http://zeus2.itb.cnr.it/~webgene/genebuilder.html

1) Predicts TATA box(i.e, TATA box pattern and position) and Poly-A site prediction(i.e, position and pattern). 2) Gives view of transcription factors.

Milanesi L, D'Angelo D, Rogozin IB. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 1999 Jul-Aug;15(7-8):612-21. PubMed PMID: 10487869.

1999

100

Gene model and Coding potential are shown graphically, but are not loading as on 25th july 2012
Gene model and Coding potential are shown graphically, but are not loading as on 25th july 2012

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 May;Chapter 4:Unit4.6. PubMed PMID: 18428701.

2003

100

1) Results can be obtained by e-mail. 2) Gene information includes the Gene number and strand type. 3) Frame information is also given.
1) Results can be obtained by e-mail. 2) Gene information includes the Gene number and strand type. 3) Frame information is also given.

GeneNest
http://genenest.molgen.mpg.de/

GeneNest is a comprehensive visualization of gene indices of the organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs.

Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M. GeneNest: automated generation and visualization of gene indices. Trends Genet. 2000 Nov;16(11):521-3. PubMed PMID: 12199289.

2000

100

GeneSplicer
http://cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml

Not available

100

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
"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"

GenomeScan
http://genes.mit.edu/genomescan.html

Predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.

Yeh RF, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome. Genome Res. 2001 May;11(5):803-16. PubMed PMID:11337476; PubMed Central PMCID: PMC311055.

2001

100

No output result obtained. PS file not supported on server and PDF file shown blank
No output result obtained. PS file not supported on server and PDF file shown blank

GenomeThreader
http://www.plantgdb.org/cgi-bin/GenomeThreader/gth.cgi

The GenomeThreader server allows you to perform spliced alignment of protein or EST/cDNA sequences to genomic DNA.

Not available

100

GENSCAN
http://genes.mit.edu/GENSCAN.html

Predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.

Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997 Apr 25;268(1):78-94. PubMed PMID: 9149143.

1997

100

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.
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.

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 Mar;17(3):280-1. PubMed PMID: 11294793.

2001

100

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
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

MAASE - Manually Annotated Alternatively Spliced Events
http://xmaase.genomics.purdue.edu/

It is a resource for convenient access, identification, and annotation of alternative splicing events (ASEs).

Zheng CL, Kwon YS, Li HR, Zhang K, Coutinho-Mansfield G, Yang C, Nair TM, Gribskov M, Fu XD. MAASE: an alternative splicing database designed for supporting splicing microarray applications. RNA. 2005 Dec;11(12):1767-76. Epub 2005 Oct 26. PubMed PMID: 16251387; PubMed Central PMCID: PMC1370865.

2005

100

Returns error "Please specify a search term." after putting in the query term
" Returns error ""Please specify a search term."" after putting in the query term "

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 Jan 1;32(Database issue):D373-6. PubMed PMID: 14681437; PubMed Central PMCID: PMC308802.

2004

100

URL not working as on 14 Dec 2012
URL not working as on 14 Dec 2012

MZEF - Michael Zhang's Exon Finder
http://rulai.cshl.edu/tools/genefinder/

Predict putative internal protein coding exons in genomic DNA sequences.

Zhang MQ. Using MZEF to find internal coding exons. Curr Protoc Bioinformatics. 2002 Aug;Chapter 4:Unit 4.2. Review. PubMed PMID: 18792940.

2002

100

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.
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.

NetPlantGene Server
http://www.cbs.dtu.dk/services/NetPGene/

Predicts splice sites using neural networks.

Not available

100

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.
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.

Plant MPSS - Plant Massively Parallel Signature Sequencing
http://mpss.udel.edu

MPSS database measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory intergenic transcripts).

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 Jan 1;34(Database issue):D731-5. PubMed PMID: 16381968; PubMed Central PMCID: PMC1347440.

2006

100

RARGE - RIKEN ArabidopsisGenome Encyclopedia
http://rarge.psc.riken.jp/a_splicing/

Sakurai T, Satou M, Akiyama K, IIDa K, Seki M, Kuromori T, Ito T, Konagaya A, Toyoda T, Shinozaki K. RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic AcIDs Res. 2005 Jan 1;33(Database issue):D647-50. PubMed PMID: 15608280; PubMed Central PMCID: PMC539968.

2005

100

Data can be browsed by the type of Alternative Splicing events only.
Data can be browsed by the type of Alternative Splicing events only.

SEE ESE - Sequence Evaluator for ESE
http://www.cbcb.umd.edu/software/SeeEse/index.html

Identifies Exon splicing enhancers.

Not available

100

1) Results can be obtained by E-mail. 2) Gives position, Motif and score as a result. 3) Graphic output can also be seen.
1) Results can be obtained by E-mail. 2) Gives position, Motif and score as a result. 3) Graphic output can also be seen.

Softberry
http://linux1.softberry.com/berry.phtml

1) Pattern based human gene structure prediction (multiple genes, both chains). 2) Find splice sites in genomic DNA using weight matrices. 3) BESTORF program analyses EST/mRNA sequences to predict potential coding fragments. 4) FGENE-SH is human gene prediction that allows to predict genes containing minor variants of donor splice sites (GC sites). 5) Looks for Pattern-based human multiple variants (alternative splicing) of potential genes in genomic DNA. 6) Finding potential 5'-, internal and 3'-coding exons. 7) Rna SPL is used for For exon-exon junctions positions in human cDNA.

Not available

100

SpliceCenter
http://projects.insilico.us/SpliceCenter/SpliceOverview.jsp

1)Displays gene splice variants and probe target locations for expression microarray platforms.A0 2)Provides a summary of splice variant coverage of multiple genes for common microarray platforms. A03)Provides high-througput analysis of peptide sequences indicating the splice variants that do / do not include the peptide.A0

Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. 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. 2008 Jul 18;9:313. PubMed PMID: 18638396; PubMed Central PMCID: PMC2491637.

2008

100

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.
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.

SpliceIT
http://www.med.auth.gr/research/spliceIT

It is is a hybrid method for splice site prediction based on probabilistic and biological inference.

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 Apr;43(2):208-17. Epub 2009 Sep 30. PubMed PMID: 19800027.

2010

100

SpliceMiner
http://projects.insilico.us/SpliceMiner/intro.jsp

SpliceMiner is a tool for querying Evidence Viewer Database (EVDB). SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format.

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 Mar 5;8:75. PubMed PMID: 17338820; PubMed Central PMCID: PMC1839109.

2007

100

1) Gene information includes chromosome number, start and end position, strand information. 2) Probe information includes Probe position.
1) Gene information includes chromosome number, start and end position, strand information. 2) Probe information includes Probe position.

SplicePredictor
http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi

Identifies potential splice sites in (plant) pre-mRNA.

Not available

100

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.
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.

SpliceView
http://zeus2.itb.cnr.it/~webgene/wwwspliceview.html

Predicts splice signals.

Not available

100

The position of acceptor and donor site is given along with intronic and exonic sequence as well as score.
The position of acceptor and donor site is given along with intronic and exonic sequence as well as score.

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 Jan;35(Database issue):D110-5. Epub 2006 Nov 1. PubMed PMID: 17082203; PubMed Central PMCID: PMC1635337.

2007

100

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.
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.