Abstract
CyanoBase provides an online resource for access to data on genomic information about the cyanobacterium Synechocystis sp. strain PCC6803. The database contains annotations for each protein-coding gene deduced from the entire nucleotide sequence of the genome, gene classification lists, and keyword and similarity search engines. Core portions of CyanoBase consist of annotations for each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. The contents of each gene were improved by updating with the results of similarity searches and by introducing references for analysis in bioinformatics. The database now contains repository facilities that store and provide experimental information, in addition to providing proposals for the function of each gene. This information should help to avoid unnecessary, overlapping experiments and should assist communication between scientists who wish to elucidate the function of putative genes on the cyanobacteria genome. The current URL of CyanoBase is http://www.kazusa.or.jp:8080/cyano/
INTRODUCTION
Cyanobacteria are prokaryotic microorganisms that carry a complete set of genes for higher plant-like oxygenic photosynthesis. The strain Synechocystis sp. PCC6803 has the advantage of being easily transformed by DNA, allowing research into the function of unknown genes through gene disruption and insertion mutational analysis. Also, since the strain can carry out photoheterotrophic growth without loss of viability, the photosynthetic-related protein genes can be disrupted to investigate their contribution to the photosynthetic pathway.
In 1996, we reported the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803, in which 3168 potential protein-coding genes were deduced (1,2). This was the first report ever of the complete structural analysis of the genome of a photo-autotrophic organism. The complete version of CyanoBase was then released and has since been maintained to offer researchers access to information present on the genome of this organism. The basic aim of this database is to supply detailed information about potential protein encoding genes through user-friendly interfaces. From 1998, we developed CyanoMutants as a repository database for the storage and distribution of information about Synechocystis sp. PCC6803 mutants.
DESCRIPTION
CyanoBase mainly consists of positional information and annotations of deduced protein genes present on the entire nucleotide sequence of the PCC6803 genome. In a recent development, the identifiers for protein genes were cross-referenced with the gi numbers, protein_id qualifiers supplied by the international DNA databases and CyanoBase ID system. Also, in order to allow users access to additional data derived from automated computer analysis, a direct link to PEDANT (3) entries has been provided for each page of the protein gene annotation.
The database contains a submission form for the deposition of mutant information, as well as repository for the proposed functions and gene names of functionally unknown or mis-annotated genes. The repository database stores and provides submitted information of an experimental nature or conjectures about the function of each gene in CyanoBase. Corresponding entries are automatically linked by cross-reference to the gene identifier. The submitted information should help to avoid unnecessary, overlapping experimental efforts and should assist scientists in their attempts to clarify the functions of putative genes in cyanobacteria.
SUPPLEMENTARY MATERIAL
See Supplementary Material available at NAR Online.
Acknowledgments
ACKNOWLEDGEMENT
This work was supported by the Kazusa DNA Research Institute Foundation.
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