Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | D353-D357 |
| Journal | Nucleic acids research |
| Volume | 41 |
| Issue number | D1 |
| DOIs | |
| Publication status | Published - Jan 1 2013 |
Fingerprint
All Science Journal Classification (ASJC) codes
- Genetics
Cite this
KEGG OC : A large-scale automatic construction of taxonomy-based ortholog clusters. / Nakaya, Akihiro; Katayama, Toshiaki; Itoh, Masumi; Hiranuka, Kazushi; Kawashima, Shuichi; Moriya, Yuki; Okuda, Shujiro; Tanaka, Michihiro; Tokimatsu, Toshiaki; Yamanishi, Yoshihiro; Yoshizawa, Akiyasu C.; Kanehisa, Minoru; Goto, Susumu.
In: Nucleic acids research, Vol. 41, No. D1, 01.01.2013, p. D353-D357.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - KEGG OC
T2 - A large-scale automatic construction of taxonomy-based ortholog clusters
AU - Nakaya, Akihiro
AU - Katayama, Toshiaki
AU - Itoh, Masumi
AU - Hiranuka, Kazushi
AU - Kawashima, Shuichi
AU - Moriya, Yuki
AU - Okuda, Shujiro
AU - Tanaka, Michihiro
AU - Tokimatsu, Toshiaki
AU - Yamanishi, Yoshihiro
AU - Yoshizawa, Akiyasu C.
AU - Kanehisa, Minoru
AU - Goto, Susumu
PY - 2013/1/1
Y1 - 2013/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84876517441&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84876517441&partnerID=8YFLogxK
U2 - 10.1093/nar/gks1239
DO - 10.1093/nar/gks1239
M3 - Article
C2 - 23193276
AN - SCOPUS:84876517441
VL - 41
SP - D353-D357
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - D1
ER -