Skip Navigation


DNA Research Advance Access originally published online on December 13, 2006
DNA Research 2006 13(6):245-254; doi:10.1093/dnares/dsl014
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Supplementary data
Right arrowOA All Versions of this Article:
13/6/245    most recent
dsl014v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (1)
Right arrow Request Permissions
Google Scholar
Right arrow Articles by Kosuge, T.
Right arrow Articles by Sugawara, H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kosuge, T.
Right arrow Articles by Sugawara, H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

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 Kosuge1, Takashi Abe1, Toshihisa Okido1, Naoto Tanaka1,2,3, Masaki Hirahata1,2, Yutaka Maruyama1,2, Jun Mashima1, Aki Tomiki1, Motoyoshi Kurokawa4, Ryutaro Himeno4, Satoshi Fukuchi1, Satoru Miyazaki1,3, Takashi Gojobori1, Yoshio Tateno1 and Hideaki Sugawara1,*

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
2 Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation (JST) Chiyoda-ku, Tokyo 102-8666, Japan
3 Faculty of Pharmaceutical Science, Tokyo University of Science, Noda Chiba 278-8510, Japan
4 Advanced Center for Computing and Communication, RIKEN, Wako Saitama 351-0198, Japan

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.

Key words: comparative genome; gene prediction; annotation; gene grading; bacterial genome

*To whom correspondence should be addressed. Tel. +81-55-981-6895. Fax +81-55-981-6896, E-mail: hsugawar{at}genes.nig.ac.jp

Communicated by Dr Katsumi Isono


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
E. Kaminuma, J. Mashima, Y. Kodama, T. Gojobori, O. Ogasawara, K. Okubo, T. Takagi, and Y. Nakamura
DDBJ launches a new archive database with analytical tools for next-generation sequence data
Nucleic Acids Res., January 1, 2010; 38(suppl_1): D33 - D38.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
T. Abe, S. Kanaya, H. Uehara, and T. Ikemura
A Novel Bioinformatics Strategy for Function Prediction of Poorly-Characterized Protein Genes Obtained from Metagenome Analyses
DNA Res, October 3, 2009; (2009) dsp018v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori, and Y. Tateno
DDBJ with new system and face
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D22 - D24.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.