KEGG tools for classification and analysis of viral proteins.

Zhao Jin, Yoko Sato, Masayuki Kawashima, Minoru Kanehisa

Protein science : a publication of the Protein Society 2023 Dec

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The KEGG database and analysis tools (https://www.kegg.jp) have been developed mostly for understanding genes and genomes of cellular organisms. The KO (KEGG Orthology) dataset, which is a collection of functional orthologs, plays the role of linking genes in the genome to pathways and other molecular networks, enabling KEGG mapping to uncover hidden features in the genome. Although viruses were part of KEGG for some time, they were not fully integrated in the KEGG analysis tools, because the KO assignment rate is very low for virus genes. To supplement KOs a new dataset named virus ortholog clusters (VOCs) is computationally generated, covering 90% of viral proteins in KEGG. VOCs can be used, in place of KOs, for taxonomy mapping to uncover relationships of sequence similarity groups and taxonomic groups and for identifying conserved gene orders in virus genomes. Furthermore, selected VOCs are used to define tentative KOs for characterizing protein functions. Here an overview of KEGG tools is presented focusing on these extensions for viral protein analysis. © 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

Citation

Zhao Jin, Yoko Sato, Masayuki Kawashima, Minoru Kanehisa. KEGG tools for classification and analysis of viral proteins. Protein science : a publication of the Protein Society. 2023 Dec;32(12):e4820