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Nucleic Acids Research 2006 34(Web Server issue):W440-W443; doi:10.1093/nar/gkl324
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization

Tiziana Castrignanò, Raffaella Rizzi1, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo2, Paola Bonizzoni1 and Graziano Pesole3,*

Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universita' e Ricerca, CASPUR Rome, Italy 1 DISCo, University of Milan Bicocca via Bicocca degli Arcimboldi, 8, Milan, 20135, Italy 2 Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan via Celoria 26, Milan 20133, Italy 3 Dipartimento di Biochimica e Biologia Molecolare, University of Bari via Orabona, 4, Bari 70126, Italy

*To whom correspondence should be addressed. Tel: +39 080 5443588; Fax: +39 080 5443317; Email: graziano.pesole{at}biologia.uniba.it

Received February 18, 2006. Revised March 8, 2006. Accepted April 13, 2006.

Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus may give rise to multiple mRNAs and protein isoforms, showing both major and subtle structural variations, is an exceptionally versatile tool in the optimization of the coding capacity of the eukaryotic genome. The huge and continuously increasing number of genome and transcript sequences provides an essential information source for the computational detection of genes AS pattern. However, much of this information is not optimally or comprehensively used in gene annotation by current genome annotation pipelines. We present here a web resource implementing the ASPIC algorithm which we developed previously for the investigation of AS of user submitted genes, based on comparative analysis of available transcript and genome data from a variety of species. The ASPIC web resource provides graphical and tabular views of the splicing patterns of all full-length mRNA isoforms compatible with the detected splice sites of genes under investigation as well as relevant structural and functional annotation. The ASPIC web resource—available at http://www.caspur.it/ASPIC/—is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility.


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