title: 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).
abstract: 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.
authors.affiliation: 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.
authors.forename: Takehide
authors.initials: T
authors.lastname: Kosuge
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Okido
authors.forename: Naoto
authors.initials: N
authors.lastname: Tanaka
authors.forename: Masaki
authors.initials: M
authors.lastname: Hirahata
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Maruyama
authors.forename: Jun
authors.initials: J
authors.lastname: Mashima
authors.forename: Aki
authors.initials: A
authors.lastname: Tomiki
authors.forename: Motoyoshi
authors.initials: M
authors.lastname: Kurokawa
authors.forename: Ryutaro
authors.initials: R
authors.lastname: Himeno
authors.forename: Satoshi
authors.initials: S
authors.lastname: Fukuchi
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyazaki
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Tateno
authors.forename: Hideaki
authors.initials: H
authors.lastname: Sugawara
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D003628:Database Management Systems; D005798:Genes, Bacterial; D005827:Genetics, Microbial; D016680:Genome, Bacterial; D016366:Open Reading Frames; D011387:Prokaryotic Cells
chemical_list: D004269:DNA, Bacterial