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A compilation and categorization of alternative splicing resources : Finds alternative splicing in mouse
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
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
1
Predicitions downloadable or can be browsed by using UCSC genome browser.
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
98
URL working but not leading to any result page after the query has been given.
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
99
1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.
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 Sep 15;26(18):2328-33. Epub 2010 Jul 13. PubMed PMID: 20628071.
2010
99
1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried gene
ACEScan
http://genes.mit.edu/acescan/
Provides ACEScan score for orthologous human-mouse exons.
Not available
Not available
100
Gives graphical representation of all ACEScan scored exons.
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.
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/.
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.
ASAP II - Alternative Splicing Annotation Project
http://bioinfo.mbi.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 Jan;35(Database issue):D93-8. Epub 2006 Nov 15. PubMed PMID: 17108355; PubMed Central PMCID: PMC1669709.
2006
100
1) Gives Genomic expression. 2) Gives Genomic location, gene aliases etc. as gene information. 3) Orthologous genes identified by MULTIZ alignments are given. 4) Isoform sequences are given. 5) Type of exons- Alternative or Constitute are given along with genomic position and number of EST and mRNA observed. 6) Intron type- Alternative or Constitutive, 5 site, 3 site, whether canonical or not and splice type, all information is provided. 7) Alternative Splicing information is provided.
ASPic - Alternative Splicing Prediction
http://t.caspur.it/ASPIC/index.php
1) Detect the exon-intron structure of a gene. 2) Predicts constitutive and alternative splice sites.
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 Oct 5;6:244. PubMed PMID:16207377; PubMed Central PMCID: PMC1276783.
2005
100
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 site details include the intron number, chromosome number, length, donor/ acceptor score, branching site score 9) Intron table provides information about relative and absolute start as well as relative and absolute end of intron, number of EST's, chromosome number, intron class, and Donor and acceptor site. 9) Gene information includes chromosome number, strand, position and length of gene.
ASPicDB - Alterenative Splicing Prediction database
http://t.caspur.it/ASPicDB/
Castrignanò T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio De Meo A, D'Erchia AM, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G. ASPicDB: a database resource for alternative splicing analysis. Bioinformatics. 2008 May 15;24(10):1300-4. Epub 2008 Apr 3. PubMed PMID: 18388144.
2008
100
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
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.
AVATAR
http://avatar.iecs.fcu.edu.tw/
Hsu FR, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT, Cheng CY, Shih MY, Liu CH, Chen CF. AVATAR: a database for genome-wIDe alternative splicing event detection using large scale ESTs and mRNAs. Bioinformation. 2005 Apr 22;1(1):16-8. PubMed PMID: 17597845; PubMed Central PMCID: PMC1891626.
2005
100
URL not working as on 14 Dec 2012
BIPASS - Bioinformatics Pipeline Alternative Splicing Services
http://bip.umiacs.umd.edu:8080/
Lacroix Z, Legendre C, RaschID L, Snyder B. BIPASS: BioInformatics Pipeline Alternative Splicing Services. Nucleic AcIDs Res. 2007 Jul;35(Web Server issue):W292-6. Epub 2007 Jun 21. PubMed PMID: 17584795; PubMed Central PMCID: PMC1933140.
2007
100
URL not working as on 14 Dec 2012
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 Jan 1;34(Database issue):D21-4. PubMed PMID: 16381848; PubMed Central PMCID: PMC1347382.
2006
100
Url working, but gives error in result page as on 27th July 2012
EDAS - EST Derived Alternative Splicing
http://edas2.bioinf.fbb.msu.ru/
EDAS, a database of alternatively spliced human genes, contains data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them.
Nurtdinov RN, Neverov AD, Mal'ko DB, Kosmodem'ianskii IA, Ermakova EO, Ramenskii VE, Mironov AA, Gel'fand MS. [EDAS, databases of alternatively spliced human genes]. Biofizika. 2006 Jul-Aug;51(4):589-92. Russian. PubMed PMID: 16909834.
2006
100
GatExplorer - Genomic and Transcriptomic Explorer
http://bioinfow.dep.usal.es/xgate/principal.php
GATExplorer is an integrated database that combines genomic/transcriptomic visualization with nucleotide-level probe mapping.
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 Apr 29;11:221. PubMed PMID: 20429936; PubMed Central PMCID: PMC2875241.
2010
100
Gene information includes chromosome location and gene description.
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
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.
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.
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
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
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. Epub 2010 Feb 10. PubMed PMID: 20428317; PubMed Central PMCID: PMC2860896.
2010
100
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 transcripts pertaining to that gene.
GRSDB - 'G' Rich Sequences Database
http://bioinformatics.ramapo.edu/grsdb/index.php
Offers a visual comparison of G-quadruplex distribution patterns among all the alternative RNA products of a gene with the help of dynamic graphics.
Kostadinov R, Malhotra N, Viotti M, Shine R, D'Antonio L, Bagga P. GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. Nucleic AcIDs Res. 2006 Jan 1;34(Database issue):D119-24. PubMed PMID: 16381828; PubMed Central PMCID: PMC1347436.
2006
100
1) QGRS(Quadruplex forming 'G'-Rich Sequences) sequence is given.
H-DBAS - Human Transcriptome Database for Alternative Splicing
http://jbirc.jbic.or.jp/h-dbas/
Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S. H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic AcIDs Res. 2010 Jan;38(Database issue):D86-90. Epub 2009 Dec 7. PubMed PMID: 19969536; PubMed Central PMCID: PMC2808982.
2010
100
1) Gene information gives chromosome number, position and strand. 2) Results can be downloaded. 3) Splice site details are shown graphically. 4) Also shows SNP in the graph. 5) Gene expression information is given, giving tissue specific expression in Affymetrix gene chip and Agilent. 6) Also gives information about Transcript feature.
Hollywood
http://hollywood.mit.edu/hollywood/Login.php
Holste D, Huo G, Tung V, Burge CB. HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic AcIDs Res. 2006 Jan 1;34(Database issue):D56-62. PubMed PMID: 16381932; PubMed Central PMCID: PMC1347411.
2006
100
Requires login,but no option to make a new account, so as to login and use the database.
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.
PALS Db - Putative Alternative Splicing Databases
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 Jan 1;30(1):186-90. PubMed PMID: 11752289; PubMed Central PMCID: PMC99163.
2002
100
URL not working as on14 Dec 2012
PolyA_DB
http://polya.umdnj.edu/polyadb
It specializes in identification of Poly-A tail.
Zhang H, Hu J, Recce M, Tian B. PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic AcIDs Res. 2005 Jan 1;33(Database issue):D116-20. PubMed PMID: 15608159; PubMed Central PMCID: PMC540009.
2005
100
URL not working as on 14 Dec 2012
PolyA_DB 2
http://polya.umdnj.edu/PolyA_DB2
It specializes in identification of Poly-A tail.
Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D165-8. PubMed PMID: 17202160; PubMed Central PMCID: PMC1899096.
2007
100
URL not working as on 14 Dec 2012
ProSAS
http://services.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 Jan;36(Database issue):D63-8. Epub 2007 Oct 11. PubMed PMID: 17933774; PubMed Central PMCID: PMC2238869.
2008
100
1) Gene information includes chromosome number and strand information. 2) Returning database error as on 28th july 2012
Rescue-ESE
http://genes.mit.edu/burgelab/rescue-ese/
Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB. RESCUE-ESE IDentifies candIDate exonic splicing enhancers in vertebrate exons. Nucleic AcIDs Res. 2004 Jul 1;32(Web Server issue):W187-90. PubMed PMID: 15215377; PubMed Central PMCID: PMC441531.
2004
100
Gives Exonic Splicing Enhancer motifs.
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
Not available
100
SpliceCenter
http://projects.insilico.us/SpliceCenter/SpliceOverview.jsp
1)Displays gene splice variants and probe target locations for expression microarray platforms.  2)Provides a summary of splice variant coverage of multiple genes for common microarray platforms.  3)Provides high-througput analysis of peptide sequences indicating the splice variants that do / do not include the peptide. 
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.
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.
SplicePredictor
http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi
Identifies potential splice sites in (plant) pre-mRNA.
Not available
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.
SpliceView
http://zeus2.itb.cnr.it/~webgene/wwwspliceview.html
Predicts splice signals.
Not available
Not available
100
The position of acceptor and donor site is given along with intronic and exonic sequence as well as score.
SPLICY - VERSION 1.2
http://host10.bioinfo3.ifom-ieo-campus.it/splicy/
Rambaldi D, Felice B, Praz V, Bucher P, Cittaro D, Guffanti A. Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S17. PubMed PMID: 17430561; PubMed Central PMCID: PMC1885846.
2007
100
URL not working as on 14 Dec 2012
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.
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 Jan;36(Database issue):D780-6. Epub 2007 Oct 11. PubMed PMID: 17932061; PubMed Central PMCID: PMC2238884.
2008
100
 
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