| BLAT - BLAST like Alignment toolhttp://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. |
| ASAP II - Alternative Splicing Annotation Projecthttp://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 Predictionhttp://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 databasehttp://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 toolhttp://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. |
| AVATARhttp://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 |
| H-DBAS - Human Transcriptome Database for Alternative Splicinghttp://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. |
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