title: VMD: a community annotation database for oomycetes and microbial genomes.
abstract: 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 approximately 19,000 and approximately 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 approximately 1600 gene models for P.sojae and approximately 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/.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA-24061, USA.
authors.forename: Sucheta
authors.initials: S
authors.lastname: Tripathy
authors.forename: Varun N
authors.initials: VN
authors.lastname: Pandey
authors.forename: Bing
authors.initials: B
authors.lastname: Fang
authors.forename: Fidel
authors.initials: F
authors.lastname: Salas
authors.forename: Brett M
authors.initials: BM
authors.lastname: Tyler
mesh_terms: D030561:Databases, Nucleic Acid; D023281:Genomics; D020407:Internet; D010838:Phytophthora / Q000235:genetics*; D018511:Systems Integration; D014584:User-Computer Interface