Nucleic Acids Res. 2001 Jan 1;29(1):22-8.

The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV.

Source

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Abstract

The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www.ncbi.nlm.nih. gov/COG). In addition, a supplement to the COGs is available, in which proteins encoded in the genomes of two multicellular eukaryotes, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, and shared with bacteria and/or archaea were included. The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.

PMID:: 11125040; [PubMed - indexed for MEDLINE]
PMCID: PMC29819

Free PMC Article

Images from this publication.See all images (3) Free text

MeSH Terms, Substances

MeSH Terms

Substances

Proteins

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Molecular Biology Databases

Libraries

LinkOut Holdings

Supplemental Content

Related citations

The COG database: a tool for genome-scale analysis of protein functions and evolution. [Nucleic Acids Res. 2000]
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Tatusov RL, Galperin MY, Natale DA, Koonin EV. Nucleic Acids Res. 2000 Jan 1; 28(1):33-6.
The COG database: an updated version includes eukaryotes. [BMC Bioinformatics. 2003]
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. BMC Bioinformatics. 2003 Sep 11; 4:41. Epub 2003 Sep 11.
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. [Biol Direct. 2007]
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV. Biol Direct. 2007 Nov 27; 2:33. Epub 2007 Nov 27.
Review Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes. [Genetica. 1999]
Review Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.
Galperin MY, Koonin EV. Genetica. 1999; 106(1-2):159-70.
Review A genomic perspective on protein families. [Science. 1997]
Review A genomic perspective on protein families.
Tatusov RL, Koonin EV, Lipman DJ. Science. 1997 Oct 24; 278(5338):631-7.

See reviews... See all...

Cited by over 100 PubMed Central articles

Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. [PLoS Genet. 2011]
Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.
Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, et al. PLoS Genet. 2011 Dec; 7(12):e1002430. Epub 2011 Dec 22.
Genome characterization of the oleaginous fungus Mortierella alpina. [PLoS One. 2011]
Genome characterization of the oleaginous fungus Mortierella alpina.
Wang L, Chen W, Feng Y, Ren Y, Gu Z, Chen H, Wang H, Thomas MJ, Zhang B, Berquin IM, et al. PLoS One. 2011; 6(12):e28319. Epub 2011 Dec 8.
Identifying single copy orthologs in Metazoa. [PLoS Comput Biol. 2011]
Identifying single copy orthologs in Metazoa.
Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P. PLoS Comput Biol. 2011 Dec; 7(12):e1002269. Epub 2011 Dec 1.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.
Cited in Books
NCBI Bookshelf books that cite the current articles.

Recent activity

Clear Turn Off Turn On

The COG database: new developments in phylogenetic classification of proteins fr...
The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Nucleic Acids Res. 2001 Jan 1 ;29(1):22-8.

PubMed
Targeting of malate synthase 1 to the peroxisomes of Saccharomyces cerevisiae ce...
Targeting of malate synthase 1 to the peroxisomes of Saccharomyces cerevisiae cells depends on growth on oleic acid medium.
Eur J Biochem. 2002 Feb ;269(3):915-22.

PubMed
Evidence for the evolution of bdelloid rotifers without sexual reproduction or g...
Evidence for the evolution of bdelloid rotifers without sexual reproduction or genetic exchange.
Science. 2000 May 19 ;288(5469):1211-5.

PubMed
The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphae...
The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants.
Proc Natl Acad Sci U S A. 2002 Aug 20 ;99(17):11275-80. Epub 2002 Aug 2 .

PubMed
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory st...
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
J Bacteriol. 2002 Oct ;184(19):5479-90.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: