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Nucleic Acids Research Advance Access published online on November 5, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp912
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© The Author(s) 2009. Published by Oxford University Press.
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

The comprehensive microbial resource

Tanja Davidsen1,*, Erin Beck1, Anuradha Ganapathy2, Robert Montgomery1, Nikhat Zafar1, Qi Yang1, Ramana Madupu1, Phil Goetz1, Kevin Galinsky1, Owen White2 and Granger Sutton1

1J. Craig Venter Institute, Rockville, MD 20850 and 2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA

*To whom correspondence should be addressed. Tel: +1-301-795-7823; Fax: +1-301-294-3142; Email: tanjad{at}jcvi.org

Received August 20, 2009. Revised October 6, 2009. Accepted October 7, 2009.

The Comprehensive Microbial Resource or CMR (http://cmr.jcvi.org) provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to displaying the original annotation from GenBank, the CMR makes available secondary automated structural and functional annotation across all genomes to provide consistent data types necessary for effective mining of genomic data. Precomputed homology searches are stored to allow meaningful genome comparisons. The CMR supplies users with over 50 different tools to utilize the sequence and annotation data across one or more of the 571 currently available genomes. At the gene level users can view the gene annotation and underlying evidence. Genome level information includes whole genome graphical displays, biochemical pathway maps and genome summary data. Comparative tools display analysis between genomes with homology and genome alignment tools, and searches across the accessions, annotation, and evidence assigned to all genes/genomes are available. The data and tools on the CMR aid genomic research and analysis, and the CMR is included in over 200 scientific publications. The code underlying the CMR website and the CMR database are freely available for download with no license restrictions.


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