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. 2007 Jan;35(Database issue):D339-42.
doi: 10.1093/nar/gkl1004. Epub 2006 Dec 7.

Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes

Masaki Hirahata  1 , Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara
Affiliations

Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes

Masaki Hirahata et al. Nucleic Acids Res. 2007 Jan.

Abstract

Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at http://gib-v.genes.nig.ac.jp/.

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Figures

Figure 1
Figure 1
Schema of Genome Information Broker for Viruses (GIB-V). This schema shows the system architecture and the data flow of GIB-V. The hardware components of GIB-V are a World Wide Web server, relational database server and homology search server.
Figure 2
Figure 2
Example of BLAST search results. blastp was executed for the ‘All family’ sequence. The query is an RNA-dependent RNA-polymerase of Human astrovirus. (a) Search result as it appears with ‘Graphic View’ indicated. The upper part of the page shows the result displayed graphically, and the lower part shows the result in text form. (b) Search result as it appears with ‘Feature List’ indicated. Clicking the ‘Set Query’ button activates ClustalW and sends sequence data automatically. (c) The ClustalW page. Data has been submitted from the Feature List.
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