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

By R. Tatusov, D. Natale, I. Garkavtsev, Tatiana A. Tatusova, U. Shankavaram, B. S. Rao, B. Kiryutin, Michael Y. Galperin, N. Fedorova, Eugene V. Koonin. Nucleic Acids Res., 2001

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Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ecf1848db9f0e81a8a0dbffeb8162772cb6be733

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Citations in the corpus

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough (2011, methodology): “Despite the great progress in software development [19–22,52–54], our nine years of experience with large-scale multigene analyses [55] leads us to conclude that computer-assisted manual expertise is not yet dispensable.”
Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota (2008, neutral): “gov/COG/">NCBI COGs database (see Further information”
STRING: a database of predicted functional associations between proteins (2003, methodology): “Previous genomic context databases such as Indigo (13), the first version of STRING (14), the Clusters of Orthologous Group (COG) database (15), Predictome (16), and SNAPper (17) only rely on a single form of genomic”
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments (2010, methodology): “These simulations were derived from diverse gene families that arise in genome-scale studies (‘‘Collections of Orthologous Groups’’ or COGs, [20]).”
CDD: conserved domains and protein three-dimensional structure (2012, methodology): “We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI’s Protein Clusters database for providing such vital resources.”
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 (2001, background): “edu ), against the COG database to find putative orthologues in other completed genome”
VFDB: a reference database for bacterial virulence factors (2004, methodology): “The Clusters of Orthologous Group (COG) (11) database was used to make classiﬁcation for each gene record in the database if there lacks such information in their original annotation ﬁles.”
Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses (2002, background): “QuartOPs are similar to the clusters of orthologous groups (COGs) maintained by the NCBI [26–28], but differ in that COGs require only unidirectional, circular best hit relationships for three of the reference genomes, whereas we require the reciprocal top hit relationship for the four genomes…”
KAAS: an automatic genome annotation and pathway reconstruction server (2007, methodology): “In practice, they are computationally deduced from the bi-directional best hit (BBH) relationship in pairwise genome comparison (7, 8 ).”
Handbook of Corynebacterium glutamicum (2005, methodology): “© 2005 by Taylor & Francis Group, LLC COG (cluster of orthologous groups) system [41].”
An efficient algorithm for large-scale detection of protein families. (2002, methodology): “Some of these methods rely on manual intervention for family assignment of multi-domain proteins (24).”
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix (2009, methodology): “We obtained sequences of members of Clusters of Orthologous Groups (COG) gene families (Tatusov et al. 2001) and members of Pfam PF00005 (Finn et al. 2006) from the fall 2007 release of the MicrobesOnline database (http://www.microbesonline.org/).”
The properties of protein family space depend on experimental design (2005, methodology): “For TRIBES and COGs two possible trend lines are shown: linear as a bold line with the expression in bold font for the fit at the top left corner and logarithmic as a dotted line with the expression in regular font at the bottom right corner.”