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About CyanoBase

Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell.

CyanoBase is genome database for cyanobacteria and provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. This database was originally developed by Makoto Hirosawa, Takakazu Kaneko and Satoshi Tabata, and the current version of CyanoBase has been developed by Mitsuteru Nakao, Shinobu Okamoto, Takatomo Fujisawa, Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata at Kazusa DNA Research Institute. Currently, CyanoBase has been maintained at Yasukazu Nakamura’s Laboratory of National Institute of Genetics since 2011.

Publications

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

Fujisawa T, Narikawa R, Maeda SI, Watanabe S, Kanesaki Y, Kobayashi K, Nomata J, Hanaoka M, Watanabe M, Ehira S, Suzuki E, Awai K, Nakamura Y.

Nucleic Acids Research 2017; doi: 10.1093/nar/gkw1131 https://academic.oup.com/nar/article-pdf/45/D1/D551/8846945/gkw1131.pdf

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

Fujisawa T, Okamoto S, Katayama T, Nakao M, Yoshimura H, Kajiya-Kanegae H, Yamamoto S, Yano C, Yanaka Y, Maita H, Kaneko T, Tabata S, Nakamura Y.

Nucleic Acids Research 2014; doi: 10.1093/nar/gkt1145 http://nar.oxfordjournals.org/content/42/D1/D666.full.pdf PDF

CyanoBase: the cyanobacteria genome database update 2010

Mitsuteru Nakao; Shinobu Okamoto; Mitsuyo Kohara; Tsunakazu Fujishiro; Takatomo Fujisawa; Shusei Sato; Satoshi Tabata; Takakazu Kaneko; Yasukazu Nakamura

Nucleic Acids Research 2009; doi: 10.1093/nar/gkp915 http://nar.oxfordjournals.org/cgi/reprint/gkp915?ijkey=PJZqc13V5F9NF5A&keytype=ref PDF

CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000.

Nakamura Y, Kaneko T, Tabata S.

Nucleic Acids Res. 2000 Jan 1; 28(1): 72. http://nar.oxfordjournals.org/cgi/reprint/28/1/72 PDF

Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803.

Nakamura Y, Kaneko T, Miyajima N, Tabata S.

Nucleic Acids Res. 1999 Jan 1; 27(1): 66-68. http://nar.oxfordjournals.org/cgi/reprint/27/1/66 PDF

CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803.

Nakamura Y, Kaneko T, Hirosawa M, Miyajima N, Tabata S.

Nucleic Acids Res. 1998 Jan 1; 26(1): 63-67. http://nar.oxfordjournals.org/cgi/reprint/26/1/63 PDF

Cyanobase: The Genome Database for Synechocystis sp. strain PCC6803

Nakamura, Y., Miyajima, N., Hirosawa, M., Kaneko, T., Tabata, S.

in Proc. Seventh Workshop on Genome Informatics 1996; 214-215.

Cyanobase: Visual presentation of information on the genome of Cyanobacterium Synechocystis sp. strain PCC6803 through WWW.

Hirosawa, M., Kaneko, T., Tabata, S.

in Proceedings of Genome Informatics Workshop 1995, 102-103.

Topics

News and release notes for CyanoBase.

2012-12-01

• Updated the definition and gene symbols in cyanobacteria desaturases, suggested from Dr. Norio Murata.

2011年6月

Transfer of database from Kazusa DNA Research Institute to National Institute of Genetics

2009-12-24

• System Maintenance Notice (09:00 - 16:00 JST)

2009-11-28

• Updated the gene_symbol search index to remove wrong records.
• Released new GeneView cache system to improve display speed. See http://genome.kazusa.or.jp/cyanobase/Synechocystis/genes/slr1311

2009-10-30

• New cyanobase paper published at NAR Database Issue 2010. CyanoBase: the cyanobacteria genome database update 2010 – Nakao et al., 10.1093/nar/gkp915 – Nucleic Acids Research

2009-09-25

• New version released. In this version contains following features: (1) expanded full text search, (2) Gene Indexing based references, (3) Genes and Mutants (as known as CyanoGenes/Mutants), and (4) InterProScan summary.

2009-05-11

• The N-terminal sequence of hoxF (sll1221) was updated to reflect the reference (<PMID:12034472>) and GenBank file (GI:1771717).

2009-02-13

• The new CyanoBase released.

2008-10-03

• Preview new CyanoBase released.

2008-08-12

• A database of the Nostoc punctiforme ATCC 29133 genome was set up.

2008-08-11

• A database of the Cyanothece sp. ATCC 51142 genome was set up.

2008-08-06

• A database of the Prochlorococcus marinus str. MIT 9211 genome was set up.

2008-08-05

• A database of the Synechococcus sp. WH 7803 genome was set up.
• A database of the Prochlorococcus marinus str. MIT 9215 genome was set up.

2008-08-04

• All of the predicted proteins in CyanoBase were subjected to similarity search against the following databases. Each one is shown on the gene information page.

2008-07-18

• A database of the Synechococcus sp. RCC307 genome was set up.

2008-07-17

• A database of the Prochlorococcus marinus str. MIT 9301 genome was set up.
• A database of the Prochlorococcus marinus str. NATL1A genome was set up.

2008-07-16

• A database of the Prochlorococcus marinus str. MIT 9303 genome was set up.

2008-07-15

• A database of the Prochlorococcus marinus str. MIT 9515 genome was set up.

2008-07-11

• A database of the Prochlorococcus marinus str. AS9601 genome was set up.

2008-07-10

• A database of the Synechococcus sp. JA-3-3Ab genome was set up.

2008-07-09

• A database of the Synechococcus sp. JA-2-3B’a(2-13) genome was set up.

2008-07-08

• A database of the Synechococcus elongatus PCC 7942 genome was set up.

2008-07-04

• A database of the Prochlorococcus marinus str. MIT 9312 genome was set up.

2008-06-30

• A database of the Synechococcus sp. CC9605 genome was set up.

2008-06-26

• A database of the Synechococcus sp. CC9902 genome was set up.

2008-06-25

• A database of the Anabaena variabilis ATCC 29413 genome was set up.

2008-06-24

• A database of the Prochlorococcus marinus str. NATL2A genome was set up.

2008-05-23

• A database of the Microcystis aeruginosa NIES-843 genome was updated.

2008-05-12

• A database of the Synechococcus sp. PCC 7002 genome was set up.
• A database of the Acaryochloris marina MBIC11017 genome was set up.

2008-01-24

• All of the predicted proteins in CyanoBase were subjected to similarity search against the following databases. Each one is shown on the gene information page.

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Acknowledgement

We thank Dr. Goto and KEGG project team for providing a browser for “Gene Category List” which is originally developed for KEGG by Dr. Akiyama, Institute for Chemical Research, Kyoto University.

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Links

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