MicrobesOnline: an integrated portal for comparative functional genomics

The Virtual Institute for Microbial Stress and Survival (VIMSS, http://vimss.lbl.gov) funded by the Dept. of Energy's Genomics:GTL Program, is dedicated to using integrated environmental, functional genomic, and comparative sequence and phylogeny data to understand mechanisms by which microbes survive in uncertain environments while carrying out processes of interest for bioremediation and energy generation. To support this work, VIMSS has developed a Web portal with an underlying database and analyses for comparative functional genomics of bacteria and archaea. Since 2003 MicrobesOnline (http://www.microbesonline.org) has been enabling comparative genome analysis and currently includes 465 complete genomes, of which 423 are microbial, and offers a suite of analysis and tools including: a multi-species genome browser, operon and regulon prediction methods and results, a combined gene and species phylogeny browser, a gene ontology browser, a workbench for sequence analysis (including sequence motif detection, motif searches, sequence alignment and phylogeny reconstruction), and capabilities for community annotation of genomes. Gene expression data and regulatory sequence motif detection in of themselves can be powerful tools for generating molecular function and system hypothesis. Moreover, these methods can be combined to provide additional support for a sequence motif or expression profile similarity alone. Work is in progress on incorporating additional publicly available microarray experiment datasets from a wider taxonomic sampling of microorganisms, enabling comparative phylogeny methods in the context of sequence motifs and expression profiles. In the face of a growing number of datasets and computational methods, MicrobesOnlines serves an important integrative role at both the experimental data and the computational biology software levels. We invite new and old users to try out our new web enabled computational tools and rich microbial dataset environment. 1