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).
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.
Kosuge
Takehide
T
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.
Abe
Takashi
T
Okido
Toshihisa
T
Tanaka
Naoto
N
Hirahata
Masaki
M
Maruyama
Yutaka
Y
Mashima
Jun
J
Tomiki
Aki
A
Kurokawa
Motoyoshi
M
Himeno
Ryutaro
R
Fukuchi
Satoshi
S
Miyazaki
Satoru
S
Gojobori
Takashi
T
Tateno
Yoshio
Y
Sugawara
Hideaki
H
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
D004269:DNA, Bacterial