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Inferring Antimicrobial Resistance from Pathogen Genomes in KEGG

  • Minoru KanehisaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1807)

Abstract

The KEGG database is widely used as a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It contains, among others, KEGG pathway maps and BRITE hierarchies (ontologies) representing high-level systemic functions of the cell and the organism. By the processes called pathway mapping and BRITE mapping, information encoded in the genome, especially the repertoire of genes, is converted to such high-level functional information. This general methodology can be applied to microbial genomes to infer antimicrobial resistance (AMR), which is becoming an increasingly serious threat to the global public health. Here we present how knowledge on AMR is accumulated in the KEGG Pathogen resource and how such knowledge can be utilized by BlastKOALA and other web tools.

Key words

Beta-lactamase KEGG Orthology (KO) KEGG module Genome annotation BlastKOALA 

Notes

Acknowledgments

This work was partially supported by the National Bioscience Database Center of the Japan Science and Technology Agency. The computational resource for developing and servicing KEGG is provided by the Bioinformatics Center, Institute for Chemical Research, Kyoto University.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute for Chemical ResearchKyoto UniversityUjiJapan

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