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

Michael Y Galperin1, Yuri I Wolf1, Kira S Makarova1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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|November 9, 2020
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Summary

The updated Clusters of Orthologous Genes (COG) database now includes 1187 bacteria and 122 archaea genomes. This version features enhanced annotations, new protein families, and improved access for researchers studying microbial genomics.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial Biology

Background:

  • The Clusters of Orthologous Genes (COG) database, established in 1997, has undergone several updates.
  • Previous versions provided a framework for analyzing microbial proteomes based on gene orthology.

Purpose of the Study:

  • To present a substantially expanded and updated version of the COG database.
  • To incorporate new genomic data and enhance the functional annotation of protein families.

Main Methods:

  • Inclusion of complete genomes from 1187 bacteria and 122 archaea.
  • Replacement of deprecated gene index (gi) numbers with stable RefSeq or GenBank/ENA/DDBJ coding sequence (CDS) accession numbers.
  • Updating annotations for over 200 protein families with references and PDB links.

Main Results:

  • The current release comprises 4877 COGs, covering 1187 bacterial and 122 archaeal genomes.
  • Introduction of 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis.
  • Enhanced database accessibility via a web page and FTP, with updated functional system and pathway groupings.

Conclusions:

  • The expanded COG database offers a more comprehensive resource for comparative genomics and functional analysis of microbial proteins.
  • Future development will focus on archaeal COGs (arCOGs) and refining existing annotations for greater accuracy and utility.