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Nucleic Acids Research 2006 34(Database Issue):D46-D55; doi:10.1093/nar/gkj031
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Nucleic Acids Research, 2006, Vol. 34, Database issue D46-D55
© 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{at}oxfordjournals.org

Article

ASD: a bioinformatics resource on alternative splicing

Stefan Stamm1, Jean-Jack Riethoven, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Yesheng Tang1, Nuno L. Barbosa-Morais2 and Thangavel Alphonse Thanaraj*

European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD, UK 1University of Erlangen, Institute for Biochemistry Fahrstrasse 17, 91054 Erlangen, Germany 2Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon 1649-028 Lisbon, Portugal

*To whom correspondence should be addressed. Tel: +44 1223 494650; Fax: +44 1223 494468; Email: thanaraj{at}ebi.ac.uk

Received August 23, 2005. Revised September 22, 2005. Accepted September 22, 2005.

Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. We present the continuation and upgrade of the ASD [T. A. Thanaraj, S. Stamm, F. Clark, J. J. Riethoven, V. Le Texier, J. Muilu (2004) Nucleic Acids Res. 32, D64–D69] that consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs. ASD includes a workbench, which is an analysis tool that enables users to carry out splicing related analysis such as characterization of introns for various splicing signals, identification of splicing regulatory elements on a given RNA sequence, prediction of putative exons and prediction of putative translation start codons. The different ASD modules are integrated and can be accessed through user-friendly interfaces and visualization tools. ASD data has been integrated with Ensembl genome annotation project as a Distributed Annotation System (DAS) resource and can be viewed on Ensembl genome browser. The ASD resource is presented at (http://www.ebi.ac.uk/asd).


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