Automated interpretation of metabolic capacity from genome and metagenome sequences

Abstract

The KEGG pathway maps are widely used as a reference data set for inferring high-level functions of the organism or the ecosystem from its genome or metagenome sequence data. The KEGG modules, which are tighter functional units often corresponding to subpathways in the KEGG pathway maps, are designed for better automation of genome interpretation. Each KEGG module is represented by a simple Boolean expression of KEGG Orthology (KO) identifiers (K numbers), enabling automatic evaluation of the completeness of genes in the genome. Here we focus on metabolic functions and introduce reaction modules for improving annotation and signature modules for inferring metabolic capacity. We also describe how genome annotation is performed in KEGG using the manually created KO database and the computationally generated SSDB database. The resulting KEGG GENES database with KO (K number) annotation is a reference sequence database to be compared for automated annotation and interpretation of newly determined genomes.

Keywords

metabolic pathway / functional module / genome annotation / genome interpretation / KEGG database

References

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ACKNOWLEDGMENTS

This work was partially supported by the Japan Science and Technology Agency. The computational resource was provided by the Bioinformatics Center, Institute for Chemical Research, Kyoto University.

CONFLICT OF INTEREST

The author Minoru Kanehisa declares that no conflict of interest exists.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg