KEGG OC: A large-scale automatic construction of taxonomy-based ortholog clusters

Akihiro Nakaya, Toshiaki Katayama, Masumi Itoh, Kazushi Hiranuka, Shuichi Kawashima, Yuki Moriya, Shujiro Okuda, Michihiro Tanaka, Toshiaki Tokimatsu, Yoshihiro Yamanishi, Akiyasu C. Yoshizawa, Minoru Kanehisa, Susumu Goto

研究成果: Contribution to journalArticle査読

78 被引用数 (Scopus)

抄録

The identification of orthologous genes in an increasing number of fully sequenced genomes is a challenging issue in recent genome science. Here we present KEGG OC (http://www.genome.jp/tools/oc/), a novel database of ortholog clusters (OCs). The current version of KEGG OC contains 1 176 030 OCs, obtained by clustering 8 357 175 genes in 2112 complete genomes (153 eukaryotes, 1830 bacteria and 129 archaea). The OCs were constructed by applying the quasi-clique-based clustering method to all possible protein coding genes in all complete genomes, based on their amino acid sequence similarities. It is computationally efficient to calculate OCs, which enables to regularly update the contents. KEGG OC has the following two features: (i) It consists of all complete genomes of a wide variety of organisms from three domains of life, and the number of organisms is the largest among the existing databases; and (ii) It is compatible with the KEGG database by sharing the same sets of genes and identifiers, which leads to seamless integration of OCs with useful components in KEGG such as biological pathways, pathway modules, functional hierarchy, diseases and drugs. The KEGG OC resources are accessible via OC Viewer that provides an interactive visualization of OCs at different taxonomic levels.

本文言語英語
ページ(範囲)D353-D357
ジャーナルNucleic acids research
41
D1
DOI
出版ステータス出版済み - 1 1 2013

All Science Journal Classification (ASJC) codes

  • 遺伝学

フィンガープリント

「KEGG OC: A large-scale automatic construction of taxonomy-based ortholog clusters」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル