[Special Issue: Fact Databases and Freewares] A Useful Bioinformatics Suite for Retrieving and Analyzing Microbial Genome Data (G-InforBIO)

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  • Tanaka Naoto
    Center for Information Biology and DDBJ, National Institute of Genetics Institute for Bioinformatics Research and Development (BIRD) Faculty of Pharmaceutical Science, Tokyo University of Science
  • Abe Takashi
    Center for Information Biology and DDBJ, National Institute of Genetics SOKENDAI
  • Miyazaki Satoru
    Faculty of Pharmaceutical Science, Tokyo University of Science
  • Sugawara Hideaki
    Center for Information Biology and DDBJ, National Institute of Genetics SOKENDAI

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Other Title
  • ＜ファクトデータベース・フリーウェア特集号＞　微生物ゲノム解析ワークベンチ G-InforBIO

Abstract

We have developed the G-InforBIO for seamless integration of browse and analysis of genomic data. Major functions of the suite are database management, data retrieval, sequence data analysis and the visualization for genomics. An annotation database accommodates multiple flat files (FFs) of entries registered in the International Nucleotide Sequence Database Collaboration (INSDC, DDBJ/EMBL/GenBank) and also tab-delimited files of local data. Genome information on the imported annotation database can be readily retrievable using keyword searches. A subset of nucleotide and protein sequences can be also retrieved for the further analysis and graphical representation. The G-InforBIO includes sequence analysis programs for cluster analysis (BLASTCLUST, ClustalW, and SOM) and homology analysis (MegaBLAST, BLAST, Blat, and Sim4). The analysis can be applied to the retrieved subset and data imported from outside. The system provides a broad-ranging utilization of genome information. The suite is written in Java so that it is executable in Macintosh OSX, Windows XP, Linux, and Unix machines and will be downloadable from http://www.wdcm.org/inforbio/G-InforBIO/download.html. The instruction manual of the G-InforBIO can be browsed at http://www.wdcm.org/inforbio/G-InforBIO/manual_E/index.htm.

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