CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes | Zendy

Takatomo Fujisawa | Zendy; Shinobu Okamoto | Zendy; Toshiaki Katayama | Zendy; Mitsuteru Nakao | Zendy; Hidehisa Yoshimura | Zendy; Hiromi KajiyaKanegae | Zendy; Sumiko Yamamoto | Zendy; Chiyoko Yano | Zendy; Yuka Yanaka | Zendy; Hiroko Maita | Zendy; Takakazu Kaneko | Zendy; Satoshi Tabata | Zendy; Yasukazu Nakamura | Zendy

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CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes

Author(s) -

Takatomo Fujisawa,

Shinobu Okamoto,

Toshiaki Katayama,

Mitsuteru Nakao,

Hidehisa Yoshimura,

Hiromi KajiyaKanegae,

Sumiko Yamamoto,

Chiyoko Yano,

Yuka Yanaka,

Hiroko Maita,

Takakazu Kaneko,

Satoshi Tabata,

Yasukazu Nakamura

Publication year - 2013

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkt1145

Subject(s) - genome , database , biology , interface (matter) , computer science , computational biology , gene , genetics , pulmonary surfactant , biochemistry , gibbs isotherm

To understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. We have extended CyanoBase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed RhizoBase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. Both databases focus on the representation and reusability of reference genome annotations, which are continuously updated by manual curation. Domain experts have extracted names, products and functions of each gene reported in the literature. To ensure effectiveness of this procedure, we developed the TogoAnnotation system offering a web-based user interface and a uniform storage of annotations for the curators of the CyanoBase and RhizoBase databases. The number of references investigated for CyanoBase increased from 2260 in our previous report to 5285, and for RhizoBase, we perused 1216 references. The results of these intensive annotations are displayed on the GeneView pages of each database. Advanced users can also retrieve this information through the representational state transfer-based web application programming interface in an automated manner.

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