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A compilation and categorization of alternative splicing resources : Finds alternative splicing in rat
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
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.
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
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.
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
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
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.
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.
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.
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
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.
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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