CyanoBase: the cyanobacteria genome database update 2010

@article{Nakao2010CyanoBaseTC,
  title={CyanoBase: the cyanobacteria genome database update 2010},
  author={Mitsuteru Nakao and Shinobu Okamoto and Mitsuyo Kohara and Tsunakazu Fujishiro and Takatomo Fujisawa and Shusei Sato and Satoshi Tabata and Takakazu Kaneko and Yasukazu Nakamura},
  journal={Nucleic Acids Research},
  year={2010},
  volume={38},
  pages={D379 - D381}
}
CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, 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… 

Figures and Tables from this paper

CyanoBase: a large-scale update on its 20th anniversary
TLDR
A new large-scale update of CyanoBase, which coincides with its 20th anniversary, has expanded the number of cyanobacterial genomic sequences from 39 to 376 species and extended community-based reannotation resources through the re-annotation of Synechocystis sp.
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes
TLDR
The TogoAnnotation system is developed, offering a web-based user interface and a uniform storage of annotations for the curators of the CyanoBase and RhizoBase databases, which focus on the representation and reusability of reference genome annotations, which are continuously updated by manual curation.
E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria
E-cyanobacterium.org is an online platform providing tools for public sharing, annotation, analysis, and visualization of dynamical models and wet-lab experiments related to cyanobacteria. The
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria
TLDR
CyanoOmicsDB will provide researchers in this field with a convenient way to retrieve functional information on cyanobacterial genes and is described as a database aiming to provide comprehensive functional information for each cyanob bacterial gene.
The default cyanobacterial linked genome: an interactive platform based on cyanobacterial linkage networks to assist functional genomics
TLDR
The potential of the web tool is discussed in relation to other bioinformatics approaches based on guilty‐by‐association principles, with selected examples of networks illustrating its usefulness for genes found exclusively in cyanobacteria or in Cyanobacteria and chloroplasts.
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage
TLDR
The goal is to provide a source of cross-referenced data across multiple scales of biological organization—from the genome to the ecosystem—embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them.
The composition of the global and feature specific cyanobacterial core-genomes
TLDR
Cyanobacteria have developed individual strategies for the interaction with the environment, while other intracellular processes like the regulation of the protein homeostasis are globally conserved.
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002
TLDR
CyanOmics is the first integrated omics analysis database for cyanobacteria and should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp.
FusoBase: an online Fusobacterium comparative genomic analysis platform
TLDR
FusoBase is presented, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community.
Synergistic use of plant-prokaryote comparative genomics for functional annotations
TLDR
This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations.
...
...

References

SHOWING 1-10 OF 15 REFERENCES
CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000
TLDR
The contents of each gene were improved by updating with the results of similarity searches and by introducing references for analysis in bioinformatics, and the database now contains repository facilities that store and provide experimental information, in addition to providing proposals for the function of each genes.
Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803
CyanoBase provides internet access to the complete genomic information of the cyanobacterium Synechocystis sp. strain PCC6803. CyanoBase contains annotations to each protein-coding gene, deduced from
CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803
TLDR
CyanoBase is a database containing genomic information on the cyanobacterium Synechocystis sp.
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups
TLDR
In order to make available the rapidly accumulating information on closely related genome sequences, the interface for pairwise genome comparisons using the CGAT interface is enhanced, which allows users to see nucleotide sequence alignments of non-coding as well as coding regions.
Galaxy: a platform for interactive large-scale genome analysis.
TLDR
An interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results.
The generic genome browser: a building block for a model organism system database.
TLDR
The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.
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 (supplement).
  • T. Kaneko, S. Sato, S. Tabata
  • Biology
    DNA research : an international journal for rapid publication of reports on genes and genomes
  • 1996
The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously
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.
  • T. Kaneko, S. Sato, S. Tabata
  • Biology
    DNA research : an international journal for rapid publication of reports on genes and genomes
  • 1996
The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously
A Large-scale Protein–protein Interaction Analysis in Synechocystis sp. PCC6803
TLDR
The interaction data obtained in this study should provide new insights and novel strategies for functional analyses of genes in Synechocystis, and, additionally, genes in other cyanobacteria and plant genes of cyanobacterial origin.
InterPro: the integrative protein signature database
TLDR
The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs.
...
...