A genomic perspective on protein families.

By R. Tatusov, Eugene V. Koonin, David J. Lipman. 1997

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Citations in the corpus

Evolution of resilience in protein interactomes across the tree of life (2018, background): “(A) A hypothetical phylogenetic tree illustrates a speciation event that gives rise to two lineages according to the speciation-divergence model (11) and leads to present-day organisms “1” (green) and “2” (pink).”
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “An Orthologous Group (OG) is defined as a cluster of three or more homologous sequences that diverge from the same speciation event (16,17).”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “These findings stimulated the development of the notion of clusters of orthologous genes (COGs) and methods for their identification (33,34).”
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences (2013, methodology): “Any functional classification scheme can be used with PICRUSt; here, we demonstrate the use of the popular KEGG Orthology (KOs) 26 and Clusters of Orthologs Groups (COGs) 27 classification schemes.”
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. (2000, unknown): “One looks at the pattern of hits amongst different phylogenetic groups (Tatusov et al ., 1997).”
COG database update: focus on microbial diversity, model organisms, and widespread pathogens (2020, background): “erroneously marked as pseudogenes) or not encoded in the genome at all (1,3,4,58).”
Prolinks: a database of protein functional linkages derived from coevolution (2004, methodology): “The confidence metric for each prediction is derived from COG pathway recovery [22].”
The COG database: an updated version includes eukaryotes (2003, methodology): “The approach to the identification of orthologous protein sets based on clustering of consistent BeTs has been implemented in the collection of Clusters of Orthologous Groups (COGs) of proteins [9,15].”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, methodology): “Of these, 446 (31%) have at least one putative molecular function defined on the basis of sequence (such as the presence of a predicted DNA-binding domain or an enzymatic motif) in the Clusters of Orthologous Groups (COGs) of proteins catalog [27].”
Primer on the Gene Ontology (2016, methodology): “unt the evolutionary relationships among genes. Most of these methods rely on orthology (ISO evidence code), because the function of orthologs tends to be more conserved across species than paralogs (23, 24). In a typical analysis, characterised and uncharacterised genes are clustered based on seque”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, background): “The ‘Ortholog Conjecture’ states that ancestral functions are more likely to be retained between orthologous genes than between paralogs, those descended from the same gene duplication event (Tatusov et al. 1997).”
Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis (2006, background): “Briefly, the gatB gene encodes aspartyl/glutamyl-tRNA amidotransferase subunit B that synthesizes charged tRNAs in organisms lacking certain tRNA synthetases; coxA encodes a catalytic subunit of cytochrome oxidase of the respiratory chain; hcpA encodes a functionally uncharacterized protein whose le”
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes (2007, methodology): “; BLAST-based methods include Reciprocal Best Hit (RBH), COG (Cluster of Orthologous Groups)”
Comparative genomics, minimal gene-sets and the last universal common ancestor (2003, background): “These are based on the identification of groups of genes from different genomes, the sequences of which are more similar to each other than they are to other sequences from the group of genomes analyse”