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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp919
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© Published by Oxford University Press 2009.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

MicrobesOnline: an integrated portal for comparative and functional genomics

Paramvir S. Dehal1,2,*, Marcin P. Joachimiak1,2, Morgan N. Price1,2, John T. Bates1,2,3, Jason K. Baumohl1,2, Dylan Chivian1,2,3, Greg D. Friedland1,2,3, Katherine H. Huang1,2, Keith Keller1,2, Pavel S. Novichkov1,2, Inna L. Dubchak1,2, Eric J. Alm1,4 and Adam P. Arkin1,2,3,5

1Virtual Institute for Microbial Stress and Survival, 2Lawrence Berkeley National Laboratory, Berkeley, CA 94720, 3DOE Joint BioEnergy Institute, 4Department of Biological Engineering and Department of Civil Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, 5Department of Biological Engineering and 6Department of Bioengineering, University of California, Berkeley, CA, 94720, USA

*To whom correspondence should be addressed. Tel: +1 510 643 3722; Email: psdehal{at}lbl.gov

Received September 18, 2009. Accepted October 7, 2009.

Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

The authors wish it to be known that, in their opinion the first and the ninth author should be regarded as joint First Authors.


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