Skip Navigation

Nucleic Acids Research 2006 34(Web Server issue):W440-W443; doi:10.1093/nar/gkl324
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (127K) Freely available
Right arrow Screen PDF (177K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Castrignanò, T.
Right arrow Articles by Pesole, G.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Castrignanò, T.
Right arrow Articles by Pesole, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
T. Castrignano, M. D'Antonio, A. Anselmo, D. Carrabino, A. D'Onorio De Meo, A. M. D'Erchia, F. Licciulli, M. Mangiulli, F. Mignone, G. Pavesi, et al.
ASPicDB: A database resource for alternative splicing analysis
Bioinformatics, May 15, 2008; 24(10): 1300 - 1304.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Foissac and M. Sammeth
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W297 - W299.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.