Nucleic Acids Research, 2000, Vol. 28, No. 1 33-36
© 2000 Oxford University Press
The COG database: a tool for genome-scale analysis of protein functions and evolution
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www.ncbi.nlm.nih.gov/COG ). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56–83% of the gene products from each of the complete bacterial and archaeal genomes and ~35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.
* To whom correspondence should be addressed. Tel: +1 301 435 5913; Fax: +1 301 480 9241; Email: koonin@ncbi.nlm.nih.gov
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W. H. Majoros, M. Pertea, and S. L. Salzberg Efficient implementation of a generalized pair hidden Markov model for comparative gene finding Bioinformatics, May 1, 2005; 21(9): 1782 - 1788. [Abstract] [Full Text] [PDF]
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S. Huang and E. K. O'Shea A Systematic High-Throughput Screen of a Yeast Deletion Collection for Mutants Defective in PHO5 Regulation Genetics, April 1, 2005; 169(4): 1859 - 1871. [Abstract] [Full Text] [PDF]
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S.-V. Albers and A. J. M. Driessen Analysis of ATPases of putative secretion operons in the thermoacidophilic archaeon Sulfolobus solfataricus Microbiology, March 1, 2005; 151(3): 763 - 773. [Abstract] [Full Text] [PDF]
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P. Stothard and D. S. Wishart Circular genome visualization and exploration using CGView Bioinformatics, February 15, 2005; 21(4): 537 - 539. [Abstract] [Full Text] [PDF]
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G. Huang, Q. Fan, S. Lechno-Yossef, E. Wojciuch, C. P. Wolk, T. Kaneko, and S. Tabata Clustered Genes Required for the Synthesis of Heterocyst Envelope Polysaccharide in Anabaena sp. Strain PCC 7120 J. Bacteriol., February 1, 2005; 187(3): 1114 - 1123. [Abstract] [Full Text] [PDF]
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A. Montsant, K. Jabbari, U. Maheswari, and C. Bowler Comparative Genomics of the Pennate Diatom Phaeodactylum tricornutum Plant Physiology, February 1, 2005; 137(2): 500 - 513. [Abstract] [Full Text] [PDF]
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J. Kang, D. Tavakoli, A. Tschumi, R. A. Aras, and M. J. Blaser Effect of Host Species on RecG Phenotypes in Helicobacter pylori and Escherichia coli J. Bacteriol., November 15, 2004; 186(22): 7704 - 7713. [Abstract] [Full Text] [PDF]
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D. P. Zimmer, O. Paliy, B. Thomas, P. Gyaneshwar, and S. Kustu Genome Image Programs: Visualization and Interpretation of Escherichia coli Microarray Experiments Genetics, August 1, 2004; 167(4): 2111 - 2119. [Abstract] [Full Text] [PDF]
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