Microbes Online Unveils Improved Capabilities

The MicrobesOnline website for comparative and functional genomics of prokaryotes, supported by the Department of Energy (DOE) Genomics:GTL program, now includes over 420 complete genomes, with nearly 1.5 million genes assigned to more than 60,000 protein families. New capabilities of the site include an interactive tree browser for protein family phylogenies, a maximum-likelihood species tree, tools for discovering regulatory sequences, and profile searches and visualization of gene expression data. MicrobesOnline includes comprehensive protein domain, sequence family and site assignments from InterPro and COG, sequence orthology information, Gene Ontology assignments, Kyoto Enyclopedia of Genes and Genomes metabolic maps, cross-references to the Integrated Microbial Genomes (IMG) system from the Joint Genome Institute (JGI), and integrated methods for computing multiple sequence alignments and phylogenetic trees. MicrobesOnline also provides computational analyses from the Virtual Institute for Microbial Stress and Survival (VIMSS) Computational Core, including operon predictions, and gene phylogenies. And to ensure that MicrobesOnline will scale to the 1,000 complete prokaryotic genomes that are projected to be available by the end of 2007, the VIMSS Computational Core has developed an accelerated pipeline for identifying members of protein families, FastHMM.

It is increasingly rare that a single tool can lead a computational biology analysis to completion. Often the effort involved in integrating multiple methods and preparing the required datasets are the rate-limiting steps in computational biology, and thus also many biological studies. MicrobesOnline embraces interactivity, hence users can swiftly locate their genes of interest through a variety of interfaces (e.g., text search, sequence search, gene expression profile search, sequence motif search) and seamlessly submit them to a suite of computational biology methods targeted at identifying gene function, evolutionary relationships, and features of gene regulation. The most recent MicrobesOnline additions are interactive heatmaps for gene expression data, implemented as an operon-based gene expression viewer for a compendium of gene expression experiments. MicrobesOnline also allows to search for gene expression profiles similar to a given gene or operon, functionality that is designed for comparative species analysis. MicrobesOnline can incorporate microarray data for any prokaryote with at least a draft genome sequence and we encourage microarray data submissions to the site (please contact us for assistance). Finally, MicrobesOnline integrates three sequence motif tools (AlignACE, MEME, Weeder), allowing discovery of sequence motifs in user-specified sets of genes. In turn, discovered motifs can be used to search microbial genomes to identify additional candidates. These examples demonstrate the interlinked nature of MicrobesOnline analysis, an environment which allows researchers to extend or even replace custom expert analysis with a unified system embedded within a common microbial functional genomic framework.

MicrobesOnline was created by the Computational Core of the Virtual Institute for Microbial Stress and Survival (VIMSS), led by Adam Arkin at LBNL, and has been supporting comparative microbial genomics since 2003. The MicrobesOnline team members include: Eric Alm, Dylan Chivian, Paramvir Dehal, Inna Dubchak, Katherine Huang, Wayne Huang, Marcin Joachimiak, Keith Keller, and Morgan Price. The MicrobesOnline database is updated quarterly. For more information, please visit the website, read the publication*, or contact Adam Arkin.

*Eric J. Alm, Katherine H. Huang, Morgan N. Price, Richard P. Koche, Keith Keller, Inna L. Dubchak and Adam P. Arkin
The MicrobesOnline Web site for comparative genomics.
Genome Res. 2005 Jul;15(7):1015-22