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Nucleic Acids Res. 2017 Jan 4;45(D1):D551-D554. doi: 10.1093/nar/gkw1131. Epub 2016 Nov 29.

CyanoBase: a large-scale update on its 20th anniversary.

Author information

1
Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan.
2
Department of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan.
3
Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601 Japan.
4
Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan.
5
NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
6
Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
7
Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8503, Japan.
8
Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510 Japan.
9
Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami Osawa, Hachioji, Tokyo 192-0397, Japan.
10
Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan.
11
Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan yn@nig.ac.jp.

Abstract

The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research.

PMID:
27899668
PMCID:
PMC5210588
DOI:
10.1093/nar/gkw1131
[Indexed for MEDLINE]
Free PMC Article

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