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Nucleic Acids Research 2006 34(Database Issue):D379-D381; doi:10.1093/nar/gkj042
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Nucleic Acids Research, 2006, Vol. 34, Database issue D379-D381
© 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

VMD: a community annotation database for oomycetes and microbial genomes

Sucheta Tripathy, Varun N. Pandey2, Bing Fang1, Fidel Salas3 and Brett M. Tyler*

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA-24061, USA 1Department of Computer Science, Virginia Polytechnic Institute and State University Blacksburg, VA-24061, USA 2Microsoft Corporation Ltd Redmond, WA-98052, USA 3Omicia Corporation CA, USA

*To whom correspondence should be addressed. Tel: +1 540 231 7318; Fax: +1 540 231 2606; Email: bmtyler{at}vt.edu

Received August 13, 2005. Revised October 3, 2005. Accepted October 3, 2005.

The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae and Phytophthora ramorum. With the completion of the draft genome sequences of these pathogens in collaboration with the DOE Joint Genome Institute (JGI), we have created this resource to make the sequences publicly available. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with ~19 000 and ~16 000 gene models, respectively. We used two different statistical methods to validate these gene models, Fickett's and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, we could assign putative functions to 17 694 genes in P.sojae and 14 700 genes in P.ramorum. We created an easy-to-use genome browser to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are ~ 1600 gene models for P.sojae and ~700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. The database is publicly available at http://phytophthora.vbi.vt.edu/.


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