The COG database: a tool for genome-scale analysis of protein functions and evolution

By R. Tatusov, Michael Y. Galperin, D. Natale, Eugene V. Koonin. 2000

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In Molecular Biology

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BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams (2008, methodology): “BioVenn currently supports cross-references to Affymetrix [8], COG [9], Ensembl [10], EntrezGene [11], Gene Ontology [12], InterPro [13], IPI [14], KEGG Pathway [15], KOG [16], PhyloPat [17] and RefSeq [18].”
Whole-Genome Analysis of Methyl tert-Butyl Ether-DegradingBeta-Proteobacterium Methylibium petroleiphilum PM1 (2007, positive): “Analysis of Clusters of Orthologous Genes (COG) distribution (77) showed 3 that the most abundant groups (excluding no COG or general function) were amino acid 4 transport and metabolism (7.”
Who's your neighbor? New computational approaches for functional genomics (2000, background): “), each of which includes orthologs from at least three phylogenetically distant specie”
Xenobiotics shape the physiology and gene expression of the active human gut microbiome (2013, methodology): “A complementary analysis using the COG ontology (Tatusov et al., 2000) and the ShotgunFunctionalizeR package (Kristiansson et al.”
The human microbiome (2017, methodology): “The functional capacity of the metagenome can be determined by comparing predicted protein-coding genes, identified by a BLASTX search, to databases such as the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database [9] and/or COG (Clusters of Orthologous Groups of proteins) functional cate”
Circular genome visualization and exploration using CGView (2005, methodology): “The NCBI protein table format consists of eight fields of information for each gene, including location, name, unique identifier, COG functional category (Tatusov et al., 2000) and function.”
Molecular characterization of Mycobacterium abscessus strains isolated from a hospital outbreak. (2000, positive): “However, because >70% of bacterial proteins have orthologs in other organisms (60,61), one can leverage extensive knowledge of function from the model organisms to infer function for a pathogen’s genome.”
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome (2018, methodology): “We then used the program ‘anvi-run-ncbi-cogs’ to annotate genes with functions by searching them against the December 2014 release of the Clusters of Orthologous Groups (COGs) database ( Tatusov et al., 2000 ) using blastp v2.”
Structure and function of the global ocean microbiome (2015, background): “When contrasting taxonomic and functional variability in the ocean, we indeed found high taxonomic variability (even at phylum level) accompanied by relatively stable distributions of gene abundances summarized into functional categories (47) (Fig.”
Database resources of the National Center for Biotechnology Information: update (2004, background): “BLink can display subsets of these alignments by taxonomic criteria, by database of origin, relation to a complete genome, membership in a COGs (15) or by relation to a 3D structure or conserved protein domain.”
The extracytoplasmic function (ECF) sigma factors. (2002, methodology): “This view is further supported by the assignment of ECF a factors as a unique group within the conserved orthologous groups (COG) database (Tatusov et al., 2000).”
High speed BLASTN: an accelerated MegaBLAST search tool (2015, methodology): “BLAST (1,2), a heuristic search tool developed for this purpose, has found substantial applications in protein science (3) such as secondary and tertiary structure prediction (4), functional annotation (5) and orthology mapping (6), and in nucleotide science including human genome variation detectio”