Alternative splice form analysis

CONTRAST - CONditionally TRAined Search for Transcripts
http://contra.stanford.edu/contrast/

Predicts protein-coding genes from a multiple genomic alignment. It is designed for de novo predictions. It can also incorporate information from EST alignments.

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. PubMed PMID: 18096039; PubMed Central PMCID: PMC2246271.

2007

Predicitions downloadable or can be browsed by using UCSC genome browser.
Predicitions downloadable or can be browsed by using UCSC genome browser.

BDGP - Berkeley Drosophila Genome Project
http://www.fruitfly.org/seq_tools/splice.html

Used to predict the splite sites with the help of neural networks. It shows the intron/exon boundary as well.

Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM. The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics. 1999 Sep;153(1):135-77. PubMed PMID: 10471706; PubMed Central PMCID: PMC1460730.

1999

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.
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.

ECgene
http://genome.ewha.ac.kr/ECgene

Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S. ECgene: an alternative splicing database update. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D99-103. Epub 2006 Nov 28. PubMed PMID: 17132829; PubMed Central PMCID: PMC1716719.

2006

URL working but not leading to any result page after the query has been given.
URL working but not leading to any result page after the query has been given.

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.

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 Apr;12(4):656-64. PubMed PMID: 11932250; PubMed Central PMCID: PMC187518.

2002

1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.
1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.

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.

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.

Astalavista - Alternative splicing transcriptional landscape visualization tool
http://genome.crg.es/astalavista/

Identifies complex Alternative Splice events by comparing all given transcripts.

Foissac S, Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic AcIDs Res. 2007 Jul;35(Web Server issue):W297-9. Epub 2007 May 7. PubMed PMID: 17485470; PubMed Central PMCID: PMC1933205.

2007

100

1) The results can be browsed on UCSC browser. 2)Results can be downloaded in GTF or ASTA format. 3) Splice site details include the chromosome number, and the position of Alternative Splice sites. 4) Intron- Exon structure is also shown. 5) Types of Alternative Splice Events include exon skipping, alt acceptor and intron retention.
1) The results can be browsed on UCSC browser. 2)Results can be downloaded in GTF or ASTA format. 3) Splice site details include the chromosome number, and the position of Alternative Splice sites. 4) Intron- Exon structure is also shown. 5) Types of Alternative Splice Events include exon skipping, alt acceptor and intron retention.

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.

BGF - Beijing Gene Finder
http://tlife.fudan.edu.cn/bgf/

BGF is a gene finding program based onA0DP(Dynamic Programming) & HSMM(HIDden Semi-Markov Model).

Not available

100

DEDB - Drosophila melanogaster Exon Database
http://proline.bic.nus.edu.sg/dedb/index.html

It includes information on the exons of Drosophila melanogaster in a splicing graph form. A splicing graph viewer is available to visualize the splicing graph, which allows to check for the various forms of alternative splicing variants in an easy to understand way.

Lee BT, Tan TW, Ranganathan S. DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics. 2004 Dec 7;5:189. PubMed PMID: 15581431; PubMed Central PMCID: PMC538278.

2004

100

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

GeneSeqer
http://deepc2.psi.iastate.edu/cgi-bin/gs.cgi

Identify potential exon/intron structure in pre-mRNA by splice site prediction and spliced alignment.

Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5. PubMed PMID: 14764557.

2004

100

1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences.
1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences.

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"

Genie - Gene Finder Based on Generalized HIDden Markov Models
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 Fall;4(3):311-23. PubMed PMID: 9278062.

1997

100

No search option provided.
No search option provided.

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

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

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

Spidey
http://www.ncbi.nlm.nih.gov/IEB/Research/Ostell/SpIDey/

Aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing errors, or evolutionary divergence.

Wheelan SJ, Church DM, Ostell JM. SpIDey: a tool for mRNA-to-genomic alignments. Genome Res. 2001 Nov;11(11):1952-7. PubMed PMID: 11691860; PubMed Central PMCID: PMC311166.

2001

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.

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.