Automated interpretation of metabolic capacity from genome and metagenome sequences

doi:10.1007/s40484-013-0019-x

Quantitative Biology

2013, Vol. 1

Issue (3): 192-200 https://doi.org/10.1007/s40484-013-0019-x

MINI REVIEW

本期目录

Automated interpretation of metabolic capacity from genome and metagenome sequences

Minoru Kanehisa(

)

Institute for Chemical Research, Kyoto University, Uji Kyoto 611-0011, Japan

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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.

Key words： metabolic pathway functional module genome annotation genome interpretation KEGG database

收稿日期: 2013-08-15 出版日期: 2013-09-05

Corresponding Author(s): Kanehisa Minoru,Email:kanehisa@kuicr.kyoto-u.ac.jp

引用本文:

. Automated interpretation of metabolic capacity from genome and metagenome sequences[J]. Quantitative Biology, 2013, 1(3): 192-200.
Minoru Kanehisa. Automated interpretation of metabolic capacity from genome and metagenome sequences. Quant Biol, 2013, 1(3): 192-200.

链接本文:

https://academic.hep.com.cn/qb/CN/10.1007/s40484-013-0019-x
https://academic.hep.com.cn/qb/CN/Y2013/V1/I3/192

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