The Clusters of Orthologous Genes (COG) database has been a well-liked resource for comparative genomics and annotation of microbial genomes for the past 20 years. Apart from simple functional annotation of sequenced genomes, the COG have been used for tasks like (i) unifying genome annotation in groups of related organisms; (ii) identifying missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighbourhoods, which in many cases allows prediction of novel functional systems; (iv) analysis of genomic neighbourhoods; Here, we go over the fundamentals of the COG technique and go over its main benefits and shortcomings when it comes to analysing microbial genomes.
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