Virginia Bioinformatics Institute launches microbial database
Researchers at the Virginia Bioinformatics Institute at Virginia Tech have launched a publicly-available microbial database to host a range of microbial genome sequences.
The VBI Microbial Database (VMD), which is described in a recent article published in Nucleic Acids Research (1), contains genome sequence and annotation data for the plant pathogens Phytophthora sojae and Phytophthora ramorum. The purpose of the database is to make widely available to researchers the recently completed genome sequences of these pathogens as well as powerful analytical tools in one integrated resource. The work described in the paper was completed by Virginia Bioinformatics Institute researchers Sucheta Tripathy, Varun Pandey, Bing Fang, and Fidel Salas, and led by Brett Tyler, VBI professor and professor of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences at Virginia Tech.
VMD is an integrated resource that includes community annotation features, toolkits, and resources to perform complex queries of biological information. The project’s researchers created a browser, which makes it easy for users to view the genome sequence data and connect to detailed annotation pages for each sequence. The community annotation interface is available for registered members to add or edit annotations.
The database will be expanded in 2006 to include genome sequences for the fungal pathogen Alternaria brassicicola and the oomycete pathogen Hyaloperonospora parasitica, both of which can infect the model plant Arabidopsis. In addition, support for proteomic and microarray data will be added, which will be linked to the functional genomic data and the genome sequences.
P. ramorum, also known as sudden oak death, is a serious oomycete pathogen that has attacked and killed tens of thousands of oak trees in California and Oregon; P. sojae, a sister pathogen of P. ramorum, causes serious damage to soybean crops. Tyler, in conjunction with collaborators at the U.S. Department of Energy Joint Genome Institute, successfully completed the genome sequences of the pathogens in 2004.
The database can be accessed by visiting http://phytophthora.vbi.vt.edu.
(1) VMD: a community annotation database for oomycetes and microbial genomes, Nucleic Acids Research, 2006, Vol.34, D379-D381.