DNA Research Advance Access published online on December 13, 2006
DNA Research, doi:10.1093/dnares/dsl014
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1 Center for Information Biology, DNA Data Bank of Japan, National Institute of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan
* To whom correspondence should be addressed. A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.
Received June 29, 2006
Revised November 9, 2006
Full Papers
Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS)
Takehide Kosuge 1, Takashi Abe 1, Toshihisa Okido 1, Naoto Tanaka 2, Masaki Hirahata 3, Yutaka Maruyama 3, Jun Mashima 1, Aki Tomiki 1, Motoyoshi Kurokawa 4, Ryutaro Himeno 4, Satoshi Fukuchi 1, Satoru Miyazaki 5, Takashi Gojobori 1, Yoshio Tateno 1, and Hideaki Sugawara 1 *
2 Center for Information Biology, DNA Data Bank of Japan, National Institute of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan; Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation (JST), Chiyoda-ku, Tokyo 102-8666, Japan; Faculty of Pharmaceutical Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
3 Center for Information Biology, DNA Data Bank of Japan, National Institute of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan; Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation (JST), Chiyoda-ku, Tokyo 102-8666, Japan
4 Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
5 Center for Information Biology, DNA Data Bank of Japan, National Institute of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan; Faculty of Pharmaceutical Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
Hideaki Sugawara, E-mail: hsugawar{at}genes.nig.ac.jp
Abstract
Communicated by Dr Katsumi Isono
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