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A compilation and categorization of alternative splicing resources : Finds alternative splicing in cow
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
BLAT - BLAST like Alignment tool
Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PubMed PMID: 11932250; PubMed Central PMCID: PMC187518.

1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.
ASAP II - Alternative Splicing Annotation Project
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.

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
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.

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 si
ASPicDB - Alterenative Splicing Prediction database
Castrignan˛ 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.
Astalavista - Alternative splicing transcriptional landscape visualization tool
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.

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.
GOOD - Gene Oriented Ortholog Databse
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.

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 trans
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