Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Software

G-InforBIO: integrated system for microbial genomics

Naoto Tanaka123*, Takashi Abe14, Satoru Miyazaki3 and Hideaki Sugawara14

Author Affiliations

1 Center for Information Biology and DDBJ, National Institute of Genetics 1111 Yata, Mishima, Shizuoka 411-8540, Japan

2 Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation (JST), 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-8666, Japan

3 Laboratory of Information Biology, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan

4 SOKENDAI, Hayama, Kanagawa 240-0193, Japan

For all author emails, please log on.

BMC Bioinformatics 2006, 7:368  doi:10.1186/1471-2105-7-368

Published: 4 August 2006

Abstract

Background

Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs.

Results

The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses.

Conclusion

The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.