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Nucleic Acids Research 2006 34(Database Issue):D56-D62; doi:10.1093/nar/gkj048
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Nucleic Acids Research, 2006, Vol. 34, Database issue D56-D62
© 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

HOLLYWOOD: a comparative relational database of alternative splicing

Dirk Holste*, George Huo1, Vivian Tung and Christopher B. Burge

Department of Biology, Massachusetts Institute of Technology Cambridge, MA 02319, USA 1Department of Computer Science and Engineering, Massachusetts Institute of Technology Cambridge, MA 02319, USA

*To whom correspondence should be addressed. Email: holste{at}mit.edu

Received August 15, 2005. Revised September 26, 2005. Accepted October 4, 2005.

RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the HOLLYWOOD system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. HOLLYWOOD was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu.

Correspondence may also be addressed to Christopher B. Burge. Tel: +1 617 258 5997; Fax: +1 617 452 2936; Email: cburge{at}mit.edu


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