Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jan;38(Database issue):D340-5.
doi: 10.1093/nar/gkp912. Epub 2009 Nov 5.

The comprehensive microbial resource

Tanja Davidsen  1 , Erin Beck, Anuradha Ganapathy, Robert Montgomery, Nikhat Zafar, Qi Yang, Ramana Madupu, Phil Goetz, Kevin Galinsky, Owen White, Granger Sutton
Affiliations

The comprehensive microbial resource

Tanja Davidsen et al. Nucleic Acids Res. 2010 Jan.

Abstract

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
JCVI Prokaryotic Genome Annotation. The annotation pipeline begins with DNA feature identification and then goes into the cyclical process of functional annotation. Automated annotation is based on trusted and supporting evidence. Manual curation of proteins or, more often today, of trusted evidence types further strengthens the annotation pipeline and can be used when annotation is regenerated. Genomes in the CMR not originally sequenced at JCVI are deposited into the CMR after automated annotation.
Figure 2.
Figure 2.
The CMR. The CMR provides both prokaryotic genome data and analytic tools. Examples from three of the major groups of tools available are shown: Genome, Gene Page and Comparative Tools.
See this image and copyright information in PMC

References

    1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res. 2008;36:D25–D30. - PMC - PubMed
    1. Webb EC. Enzyme Nomenclature. San Diego, CA: Academic Press; 1992.
    1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000;25:25–29. - PMC - PubMed
    1. Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 2005;33:D297–D302. - PMC - PubMed
    1. Riley M. Functions of the gene products of Escherichia coli. Microbiol. Rev. 1993;57:862–952. - PMC - PubMed

Publication types