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)

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, ). However, when comparative genomics is carried out, researchers must be aware that there are protein-cod...

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Bibliographic Details
Published in:DNA research Vol. 13; no. 6; pp. 245 - 254
Main Authors: Kosuge, Takehide, Abe, Takashi, Okido, Toshihisa, Tanaka, Naoto, Hirahata, Masaki, Maruyama, Yutaka, Mashima, Jun, Tomiki, Aki, Kurokawa, Motoyoshi, Himeno, Ryutaro, Fukuchi, Satoshi, Miyazaki, Satoru, Gojobori, Takashi, Tateno, Yoshio, Sugawara, Hideaki
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 31-12-2006
Subjects:
Bacteria - classification
Bacteria - genetics
Biological and medical sciences
Computational Biology
Database Management Systems
DNA, Bacterial - genetics
Fundamental and applied biological sciences. Psychology
Genes, Bacterial
Genes. Genome
Genetics of eukaryotes. Biological and molecular evolution
Genetics, Microbial
Genome, Bacterial
Molecular and cellular biology
Molecular genetics
Open Reading Frames
Prokaryotic Cells
annotation
gene grading
gene prediction
bacterial genome
comparative genome
GTP
Prediction
Exploration
Identification
Annotation
Strain
Infection
Gene
Bacteriosis
Bacteria
Genome
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Summary: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, ). 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.
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ISSN:1340-2838
1756-1663
DOI:10.1093/dnares/dsl014