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)

被引：18

作者：

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 ^{[1
]}

机构：

[1] Grad Univ Adv Studies, Natl Inst Genet, DNA Data Bank Japan, Ctr Informat Biol, Shizuoka 4118540, Japan

[2] Japan Sci & Technol Corp, Inst Bioinformat Res & Dev, Chiyoda Ku, Tokyo 1028666, Japan

[3] Tokyo Univ Sci, Fac Pharmaceut Sci, Chiba 2788510, Japan

[4] RIKEN, Adv Ctr Comp & Commun, Wako, Saitama 3510198, Japan

来源：

DNA RESEARCH | 2006年 / 13卷 / 06期

关键词：

comparative genome; gene prediction; annotation; gene grading; bacterial genome;

D O I：

10.1093/dnares/dsl014

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.ae.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.

引用

页码：245 / 254

页数：10

共 35 条

[1] Ab initio gene identification:: prokaryote genome annotation with GeneScan and GLIMMER [J].

Aggarwal, G ;

Ramaswamy, R .

JOURNAL OF BIOSCIENCES, 2002, 27 (01) :7-14

[2] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[3] PHYLOGENETIC IDENTIFICATION AND IN-SITU DETECTION OF INDIVIDUAL MICROBIAL-CELLS WITHOUT CULTIVATION [J].

AMANN, RI ;

LUDWIG, W ;

SCHLEIFER, KH .

MICROBIOLOGICAL REVIEWS, 1995, 59 (01) :143-169

[4] The InterPro database, an integrated documentation resource for protein families, domains and functional sites [J].

Apweiler, R ;

Attwood, TK ;

Bairoch, A ;

Bateman, A ;

Birney, E ;

Biswas, M ;

Bucher, P ;

Cerutti, T ;

Corpet, F ;

Croning, MDR ;

Durbin, R ;

Falquet, L ;

Fleischmann, W ;

Gouzy, J ;

Hermjakob, H ;

Hulo, N ;

Jonassen, I ;

Kahn, D ;

Kanapin, A ;

Karavidopoulou, Y ;

Lopez, R ;

Marx, B ;

Mulder, NJ ;

Oinn, TM ;

Pagni, M ;

Servant, F ;

Sigrist, CJA ;

Zdobnov, EM .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :37-40

[5] The universal protein resource (UniProt) [J].

Bairoch, A ;

Apweiler, R ;

Wu, CH ;

Barker, WC ;

Boeckmann, B ;

Ferro, S ;

Gasteiger, E ;

Huang, HZ ;

Lopez, R ;

Magrane, M ;

Martin, MJ ;

Natale, DA ;

O'Donovan, C ;

Redaschi, N ;

Yeh, LSL .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D154-D159

[6] The complete genome sequence of Escherichia coli K-12 [J].

Blattner, FR ;

Plunkett, G ;

Bloch, CA ;

Perna, NT ;

Burland, V ;

Riley, M ;

ColladoVides, J ;

Glasner, JD ;

Rode, CK ;

Mayhew, GF ;

Gregor, J ;

Davis, NW ;

Kirkpatrick, HA ;

Goeden, MA ;

Rose, DJ ;

Mau, B ;

Shao, Y .

SCIENCE, 1997, 277 (5331) :1453-+

[7] Estimating prokaryotic diversity and its limits [J].

Curtis, TP ;

Sloan, WT ;

Scannell, JW .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (16) :10494-10499

[8] Improved microbial gene identification with GLIMMER [J].

Delcher, AL ;

Harmon, D ;

Kasif, S ;

White, O ;

Salzberg, SL .

NUCLEIC ACIDS RESEARCH, 1999, 27 (23) :4636-4641

[9] Comparative Genomics of emerging human ehrlichiosis agents [J].

Dunning Hotopp, Julie C. ;

Lin, Mingqun ;

Madupu, Ramana ;

Crabtree, Jonathan ;

Angiuoli, Samuel V. ;

Eisen, Jonathan ;

Seshadri, Rekha ;

Ren, Qinghu ;

Wu, Martin ;

Utterback, Teresa R. ;

Smith, Shannon ;

Lewis, Matthew ;

Khouri, Hoda ;

Zhang, Chunbin ;

Niu, Hua ;

Lin, Quan ;

Ohashi, Norio ;

Zhi, Ning ;

Nelson, William ;

Brinkac, Lauren M. ;

Dodson, Robert J. ;

Rosovitz, M. J. ;

Sundaram, Jaideep ;

Daugherty, Sean C. ;

Davidsen, Tanja ;

Durkin, Anthony S. ;

Gwinn, Michelle ;

Haft, Daniel H. ;

Selengut, Jeremy D. ;

Sullivan, Steven A. ;

Zafar, Nikhat ;

Zhou, Liwei ;

Benahmed, Faiza ;

Forberger, Heather ;

Halpin, Rebecca ;

Mulligan, Stephanie ;

Robinson, Jeffrey ;

White, Owen ;

Rikihisa, Yasuko ;

Tettelin, Herve .

PLOS GENETICS, 2006, 2 (02) :208-223

[10]

Elphick MR, 2005, HANDB EXP PHARMACOL, V168, P283

← 1 2 3 4 →