Nucleic Acids Research, 2001, Vol. 29, No. 1 22-28
© 2001 Oxford University Press
The COG database: new developments in phylogenetic classification of proteins from complete genomes
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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.
* To whom correspondence should be addressed. Tel: +1 301 435 5913; Fax: +1 301 480 9241; Email: koonin{at}ncbi.nlm.nih.gov
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Y. Zhao, R. E. Davis, and I.-M. Lee Phylogenetic positions of 'Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2131 - 2141. [Abstract] [Full Text] [PDF]
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 E. Brouillette, M. Hyodo, Y. Hayakawa, D. K. R. Karaolis, and F. Malouin 3',5'-Cyclic Diguanylic Acid Reduces the Virulence of Biofilm-Forming Staphylococcus aureus Strains in a Mouse Model of Mastitis Infection Antimicrob. Agents Chemother., August 1, 2005; 49(8): 3109 - 3113. [Abstract] [Full Text] [PDF]
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R. Wang, J. T. Prince, and E. M. Marcotte Mass spectrometry of the M. smegmatis proteome: Protein expression levels correlate with function, operons, and codon bias Genome Res., August 1, 2005; 15(8): 1118 - 1126. [Abstract] [Full Text] [PDF]
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L. Chen, K. Brugger, M. Skovgaard, P. Redder, Q. She, E. Torarinsson, B. Greve, M. Awayez, A. Zibat, H.-P. Klenk, et al. The Genome of Sulfolobus acidocaldarius, a Model Organism of the Crenarchaeota J. Bacteriol., July 15, 2005; 187(14): 4992 - 4999. [Abstract] [Full Text] [PDF]
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D. La and D. R. Livesay MINER: software for phylogenetic motif identification Nucleic Acids Res., July 1, 2005; 33(suppl_2): W267 - W270. [Abstract] [Full Text] [PDF]
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A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, and F. Meyer BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser Nucleic Acids Res., July 1, 2005; 33(suppl_2): W710 - W716. [Abstract] [Full Text] [PDF]
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L. Brocchieri and S. Karlin Protein length in eukaryotic and prokaryotic proteomes Nucleic Acids Res., June 10, 2005; 33(10): 3390 - 3400. [Abstract] [Full Text] [PDF]
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L. Tao, A. Schenzle, J. M. Odom, and Q. Cheng Novel Carotenoid Oxidase Involved in Biosynthesis of 4,4'-Diapolycopene Dialdehyde Appl. Envir. Microbiol., June 1, 2005; 71(6): 3294 - 3301. [Abstract] [Full Text] [PDF]
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