CyanoBase: the cyanobacteria genome database
update 2010
Mitsuteru Nakao1,2,*, Shinobu Okamoto1,2, Mitsuyo Kohara1, Tsunakazu Fujishiro1,
Takatomo Fujisawa1, Shusei Sato1, Satoshi Tabata1, Takakazu Kaneko3 and
Yasukazu Nakamura1,4
1Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0812, 2Database Center for
Lifescience, Research Organization of Information and Systems, Faculty of Engineering Bldg.12, The University
of Tokyo 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, 3Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku,
Kyoto-City 603-8555 and 4Center for Information Biology and DNA Data Bank of Japan, National Institute
of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
Received September 15, 2009; Accepted October 7, 2009
ABSTRACT
CyanoBase (http://genome.kazusa.or.jp/cyanobase)
is the genome database for cyanobacteria,
which are model organisms for photosynthesis.
The database houses cyanobacteria species infor-
mation, complete genome sequences, genome-
scale experiment data, gene information, gene
annotations and mutant information. In this
version, we updated these datasets and improved
the navigation and the visual display of the data
views. In addition, a web service API now enables
users to retrieve the data in various formats with
other tools, seamlessly.
INTRODUCTION
Cyanobacteria are prokaryotic organisms that have served
as important model organisms for studying oxygenic
photosynthesis and have played a significant role in the
Earth’s history as primary producers of atmospheric
oxygen. Synechocystis sp. PCC 6803 was the first
cyanobacteria to have its genome sequenced in 1996 (1).
CyanoBase is a comprehensive and freely accessible web
database of Cyanobacteria genome information; the data
and the web site are licensed under the Creative Commons
CC0 public domain license. The database contains the
entire 3.9Mb genome sequence of Synechocystis sp. PCC
6803 in six circular genomic molecules (chromosome
and plasmids), with a total of 3725 genes. CyanoBase
was developed as the genome database not only
for Synechocystis sp. PCC but also for the other
cyanobacteria species (2,3). CyanoGenes/mutants,
released in 1998, were designed to facilitate the sharing
of information on mutants and manual gene annotations
submitted by the research community (4). As a result of
several genome sequencing projects involving cyano-
bacteria species, CyanoBase now includes 35 completely
sequenced genomes. In addition, various genome scale
experimental datasets have been produced, includ-
ing gene expression profiles and protein–protein interac-
tion data.
In this update of the database, we have redesigned and
improved the user interface in order to support both
biologists, who work around the experiments, and
bioinformaticians, who tend to deal with emerging
genome-scale data. We have expanded the accessibility
of the data navigation based on its hierarchical nature.
We have also developed a new keyword search system to
allow the user to access deep information about the
genome. For improving reusability of the data, a web
service was released to enable processing of the data
using other tools. Useful external links were also updated
to serve an information hub for the cyanobacteria genes.
IMPROVED DATA ACCESSIBILITY
CyanoBase provides access paths to the genome and gene
information for cyanobacteria. To improve the accessibil-
ity of the data, the organization of the data was
re-arranged. CyanoBase consists of pages for viewing
each genome resource, including genome projects
(DataSetView), an individual genome project
(SpeciesView), individual chromosomes (MapView),
multiple genes (GenesView), gene function classification
(GeneCategoryView), word clouds (WordCloudView),
search results (SearchView) and individual genes
(GeneView). Pages are linked according to the hierarchy
and connectivity of the data. We also designed the navi-
gation to conform to the structure for genome informa-
tion as used by biologists.
*To whom correspondence should be addressed. Tel: +81 3 5841 6754; Fax: +81 3 5841 8090; Email: mn@kazusa.or.jp, mn@dbcls.jp
Published online 30 October 2009 Nucleic Acids Research, 2010, Vol. 38, Database issue D379–D381
doi:10.1093/nar/gkp915
� The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
The GeneView page can be reached via multiple paths
from the species page, including the (i) chromosome circle
map (MapView), (ii) gene list (GenesView), (iii) function
classification (GeneCategoryView) and (iv) search results
(SearchView). The hierarchical relationship is displayed
on every page as a breadcrumbs list in the header.
We formulated URLs to correspond to the hierarchical
navigation. For instance, the URL of the slr1311
GeneView page for Synechocystis sp. PCC 6803
is http://genome.kauzsa.or.jp/cyanobase/Synechocystis
/genes/slr1311, in which each part of the path refers
to a step in the hierarchy: the data source name
(Synechocystis), the scope name (genes) and the gene ID
(slr1311).
The word cloud is generated automatically from text
descriptions of a gene set to facilitate a visual inspection
of an outline of the gene descriptions. This view helps
users to summarize the gene set and explore related gene
sets. The word frequencies in the text of a gene description
are summed to construct a word cloud view that captures
the character of the selected gene set (Figure 1).
We also improved the keyword search feature. In a full
text search, users can now select a target data scope. The
search targets include gene symbols, definitions, function
classifications, descriptions in automatic annotations and
information on mutants.
IMPROVED DATA REPRESENTATION
In this update, we introduced several new data
representations to improve viewing of and navigation
through data.
Genome context
A graphical image of the genomic context, generated by
Gbrowse (5), indicates the length, direction and function
of the gene and the surrounding genes. It also provides the
navigation links among genes in GeneView.
TableView
TableView provides an enhanced user interface that is
sortable by column and contains related links. The
tabular representation is suitable for the species list,
BLAST hits (homologs) and InterProScan (6) matches.
It is useful to analyze intra-/inter-genomic data using
these simple statistics and rankings.
Protein domains
An image and a table of predicted InterPro functional
domains enable the user to glance at the arrangement of
the protein functional domains and peruse these
descriptions on the GeneView page. The InterPro IDs in
the table have links to lists of the genes to be matched
within or between species in CyanoBase.
Word clouds
A word cloud image of the gene function, created using
Wordle (http://www.wordle.net), provides a summarized
view of the gene function of a species on the SpeciesView
page. The graphics work as an icon of the gene function
of the species.
NEW DATA AND RESOURCES
The resources present in CyanoBase as of September 2009
are shown in Table 1. The annotations, along with the
additional genome and gene information, are accumulated
continually. Genome projects on cyanobacteria species
have produced 35 complete sequenced genomes.
CyanoBase imported the genome information from both
GenBank and the original sites of the genome projects.
We also updated the curated resources. First, we
updated 301 open reading frames (ORFs) based on
comments from the research community: 200 ORFs
were improved in the translational initiation site, 99 new
ORFs were added and 2 ORFs were deleted. Second, we
updated the functional annotations of 338 genes based on
information registered in CyanoGenes and CYORF.
Third, mutant information and curated gene descriptions
were collected directly from biologists for 1700 cases and
688 genes via CyanoMuntats. We integrated the mutant
information into the GeneView page and released the new
summary page for the mutants. Fourth, we added a
Figure 1. Word cloud links of gene annotations. The display represents the search results from the SearchView page by the keyword ‘ABC’ for
Synechocystis sp. PCC 6803 genes at SearchView page. The size of each word corresponds to the number of times it appears in the results.
Table 1. Data and annotations in CyanoBase (September 2009)
Annotation Data
Species (genome projects) 35
Nucleotides 266 584 858
Genes 117 435
Protein-coding genes 114 783
RNA genes 2652
PubMed references for genes 2260
Mutant information for 688 genes 1700
D380 Nucleic Acids Research, 2010, Vol. 38, Database issue
publication list for each gene. Publications that described
the cyanobacteria genes were curated manually and listed
on the GeneView page. The curating effort has continued
to operate on a portion of the Gene Indexing project using
KazusaAnnotation, a social genome annotation system
(http://a.kazusa.or.jp). Finally, the GeneView page now
includes genome-scale experimental data, including
protein–protein interaction data for Synechocystis sp.
PCC 6803 collected by the yeast two-hybrid method (7).
We added automated annotations for each gene on the
GeneView page. These annotations include putative
orthologs based on finding a reciprocal best hit using the
BLAST program, protein functional domains based on
the InterProScan system and a Gene Ontology gene asso-
ciation based on the ipr2go mapping. Users can browse
and analyze these data using the TableView.
Useful links were added to the GeneView external links
section, for example, to the web sites for Gclust (8) and
MBGD (9) (automated ortholog gene cluster databases)
and Fluorome (10) (a database of a large-scale analysis of
chlorophyll fluorescence kinetics). Moreover, it is possible
to link many more external databases via KEGG/GENES
(11) and LinkDB (12).
WEB SERVICES
CyanoBase provides a URL-based REST web-service
interface for reusing data with other tools and computer
programs. Data are available in several file formats:
tab-delimitered text, CSV, FastA and gff3. Tools such as
Galaxy (13), BioMart (14) and spreadsheet programs
are able to import the data seamlessly. The URLs are
indicated by the orange-colored icons and are specified
in the KazusaAPI section on the relevant pages.
The SearchView page has a special export function for
a set of genes in the search results. Users can easily obtain
the gene set in plaintext format. This gene set export
function also allows users to obtain the set of genes
belonging to a gene category on the GeneCategoryView
page.
CyanoBase also provides alternative ways to export
sequence and gene annotation data. KazusaMart
(http://mart.kazusa.or.jp), a BioMart system, is able to
filter and export the data. Also, a Gbrowse service can
be used to select and export the genome sequence and
the features, with web and DAS interfaces (5).
ACKNOWLEDGEMENTS
The authors thank Mr Manabu Yamada for generating
the data of CyanoBase. The authors thank Dr Paul
Horton for reviewing the draft manuscript.
FUNDING
Kazusa DNA Research Institute Foundation. Funding for
open access charge: Kazusa DNA Research Institute
Foundation.
Conflict of interest statement. None declared.
REFERENCES
1. Kaneko,T., Sato,S., Kotani,H., Tanaka,A., Asamizu,E.,
Nakamura,Y., Miyajima,N., Hirosawa,M., Sugiura,M.,
Sasamoto,S. et al. (1996) 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., 3,
109–136.
2. Nakamura,Y., Kaneko,T., Hirosawa,M., Miyajima,N. and
Tabata,S. (1998) CyanoBase, a www database containing the
complete nucleotide sequence of the genome of Synechocystis sp.
strain PCC6803. Nucleic Acids Res., 26, 63–67.
3. Nakamura,Y., Kaneko,T. and Tabata,S. (2000) CyanoBase, the
genome database for Synechocystis sp. strain PCC6803: status for
the year 2000. Nucleic Acids Res., 28, 72.
4. Nakamura,Y., Kaneko,T., Miyajima,N. and Tabata,S. (1999)
Extension of CyanoBase. CyanoMutants: repository of mutant
information on Synechocystis sp. strain PCC6803. Nucleic Acids
Res., 27, 66–68.
5. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A.,
Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The
generic genome browser: a building block for a model organism
system database. Genome Res., 12, 1599–1610.
6. Hunter,S., Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A.,
Binns,D., Bork,P., Das,U., Daugherty,L., Duquenne,L. et al. (2009)
InterPro: the integrative protein signature database. Nucleic Acids
Res., 37, D211–D215.
7. Sato,S., Shimoda,Y., Muraki,A., Kohara,M., Nakamura,Y. and
Tabata,S. (2007) A large-scale protein protein interaction analysis
in Synechocystis sp. PCC6803. DNA Res., 14, 207–216.
8. Sato,N. (2009) Gclust: trans-kingdom classification of proteins
using automatic individual threshold setting. Bioinformatics, 25,
599–605.
9. Uchiyama,I. (2007) MBGD: a platform for microbial comparative
genomics based on the automated construction of orthologous
groups. Nucleic Acids Res., 35, D343–D346.
10. Ozaki,H., Ikeuchi,M., Ogawa,T., Fukuzawa,H. and Sonoike,K.
(2007) Large-scale analysis of chlorophyll fluorescence kinetics in
Synechocystis sp. PCC 6803: identification of the factors involved in
the modulation of photosystem stoichiometry. Plant Cell Physiol.,
48, 451–458.
11. Kanehisa,M., Araki,M., Goto,S., Hattori,M., Hirakawa,M.,
Itoh,M., Katayama,T., Kawashima,S., Okuda,S., Tokimatsu,T.
et al. (2008) KEGG for linking genomes to life and the
environment. Nucleic Acids Res., 36, D480–D484.
12. Fujibuchi,W., Goto,S., Migimatsu,H., Uchiyama,I., Ogiwara,A.,
Akiyama,Y. and Kanehisa,M. (1998) DBGET/LinkDB: an
integrated database retrieval system. Pac. Symp. Biocomput.,
683–694.
13. Giardine,B., Riemer,C., Hardison,R.C., Burhans,R., Elnitski,L.,
Shah,P., Zhang,Y., Blankenberg,D., Albert,I., Taylor,J. et al. (2005)
Galaxy: a platform for interactive large-scale genome analysis.
Genome Res., 15, 1451–1455.
14. Haider,S., Ballester,B., Smedley,D., Zhang,J., Rice,P. and
Kasprzyk,A. (2009) BioMart Central Portal–unified access to
biological data. Nucleic Acids Res., 37, W23–W27.
Nucleic Acids Research, 2010, Vol. 38, Database issue D381
