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