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, Takashi Abe, Toshihisa Okido, Naoto Tanaka, Masaki Hirahata, Yutaka Maruyama, Jun Mashima, Aki Tomiki, Motoyoshi Kurokawa, Ryutaro Himeno, Satoshi Fukuchi, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno, Hideaki Sugawara*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)245-254
Number of pages10
JournalDNA Research
Volume13
Issue number6
DOIs
StatePublished - Mar 15 2007

Keywords

  • Annotation
  • Bacterial genome
  • Comparative genome
  • Gene grading
  • Gene prediction

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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