COG database update: focus on microbial diversity, model organisms, and widespread pathogens

By Michael Y. Galperin, Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin. Nucleic Acids Res., 2020

771 citations recorded by the source corpus.

The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI's gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/18099d2a171f4377c03ca64e213d27a0bd227f06

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Citations in the corpus

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification (2021, background): “…protein sequences are looked up in the aforementioned SQLite database comprising gene symbols, protein products, dbxrefs to UniRef100, UniRef90 and UniRef50, RefSeq, clusters of orthologous groups (COGs), Enzyme Commission (EC) categories and Gene Ontology (GO) terms [16, 17, 30–32].”
VFDB 2022: a general classification scheme for bacterial virulence factors (2021, neutral): “The existing general classification schemes such as the Gene Ontology (GO) and the Clusters of Orthologous Genes (COGs) are designed to cover entire biological processes and molecular functions of various living organisms (8,9), so they have very few categories associated with bacterial pathogenesis”