Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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

Takatomo Fujisawa  1 , Rei Narikawa  2 , Shin-Ichi Maeda  3 , Satoru Watanabe  4 , Yu Kanesaki  5 , Koichi Kobayashi  6 , Jiro Nomata  7 , Mitsumasa Hanaoka  8 , Mai Watanabe  6 , Shigeki Ehira  9 , Eiji Suzuki  10 , Koichiro Awai  2 , Yasukazu Nakamura  11
Affiliations

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

Takatomo Fujisawa et al. Nucleic Acids Res. .

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Flowchart representing data processing pipeline for CyanoBase.
Figure 2.
Figure 2.
A sample Genome Project View page resulting from the keyword search ‘Synechocystis’. The table is filterable and sortable for each column.
See this image and copyright information in PMC

References

    1. Shih P.M., Wu D., Latifi A., Axen S.D., Fewer D.P., Talla E., Calteau A., Cai F., Tandeau de Marsac N., Rippka R., et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc. Natl. Acad. Sci. U.S.A. 2013;110:1053–1058. - PMC - PubMed
    1. KanekoT. SatoS., KotaniH. TanakaA., AsamizuE. NakamuraY., MiyajimaN. HirosawaM., SugiuraM. SasamotoS., et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996;3:109–136. - PubMed
    1. Nakamura Y., Kaneko T., Hirosawa M., Miyajima N., Tabata S. CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803. Nucleic Acids Res. 1998;26:63–67. - PMC - PubMed
    1. Nakamura Y., Kaneko T., Tabata S. CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000. Nucleic Acids Res. 2000;28:72. - PMC - PubMed
    1. Nakao M., Okamoto S., Kohara M., Fujishiro T., Fujisawa T., Sato S., Tabata S., Kaneko T., Nakamura Y. CyanoBase: the cyanobacteria genome database update 2010. Nucleic Acids Res. 2010;38:D379–D381. - PMC - PubMed

Publication types

LinkOut - more resources