Literature DB >> 10803979

An automated system for genome analysis to support microbial whole-genome shotgun sequencing.

T Sakiyama1, H Takami, N Ogasawara, S Kuhara, T Kozuki, K Doga, A Ohyama, K Horikoshi.   

Abstract

We developed a semi-automated genome analysis system called GAMBLER in order to support the current whole-genome sequencing project focusing on alkaliphilic Bacillus halodurans C-125. GAMBLER was designed to reduce the human intervention required and to reduce the complications in annotating thousands of ORFs in the microbial genome. GAMBLER automates three major routines: analyzing assembly results provided by genome assembler software, assigning ORFs, and homology searching. GAMBLER is equipped with an interface for convenience of annotation. All processes and options are manipulatable through a WWW browser that enables scientists to share their genome analysis results without choosing computer platforms.

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Year:  2000        PMID： 10803979     DOI： 10.1271/bbb.64.670

Source DB:  PubMed          Journal:  Biosci Biotechnol Biochem        ISSN： 0916-8451            Impact factor:   2.043


  25 in total

1.  Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125.

Authors:  H Takami; C G Han; Y Takaki; E Ohtsubo
Journal:  J Bacteriol       Date:  2001-07       Impact factor: 3.490

2.  Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution.

Authors:  Ichiro Nakagawa; Ken Kurokawa; Atsushi Yamashita; Masanobu Nakata; Yusuke Tomiyasu; Nobuo Okahashi; Shigetada Kawabata; Kiyoshi Yamazaki; Tadayoshi Shiba; Teruo Yasunaga; Hideo Hayashi; Masahira Hattori; Shigeyuki Hamada
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

3.  The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny.

Authors:  Yoshihiko Sakaguchi; Tetsuya Hayashi; Ken Kurokawa; Keisuke Nakayama; Kenshiro Oshima; Yukako Fujinaga; Makoto Ohnishi; Eiichi Ohtsubo; Masahira Hattori; Keiji Oguma
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-15       Impact factor: 11.205

4.  Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes.

Authors:  Toshiaki Fukui; Haruyuki Atomi; Tamotsu Kanai; Rie Matsumi; Shinsuke Fujiwara; Tadayuki Imanaka
Journal:  Genome Res       Date:  2005-02-14       Impact factor: 9.043

5.  Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.

Authors:  Hidehiro Toh; Brian L Weiss; Sarah A H Perkin; Atsushi Yamashita; Kenshiro Oshima; Masahira Hattori; Serap Aksoy
Journal:  Genome Res       Date:  2005-12-19       Impact factor: 9.043

6.  Complete genome sequence of Bacillus cereus NC7401, which produces high levels of the emetic toxin cereulide.

Authors:  Akira Takeno; Akira Okamoto; Keizo Tori; Kenshiro Oshima; Hideki Hirakawa; Hidehiro Toh; Norio Agata; Keiko Yamada; Naotake Ogasawara; Tetsuya Hayashi; Tohru Shimizu; Satoru Kuhara; Masahira Hattori; Michio Ohta
Journal:  J Bacteriol       Date:  2012-09       Impact factor: 3.490

7.  Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.

Authors:  Hideto Takami; Yoshihiro Takaki; Ikuo Uchiyama
Journal:  Nucleic Acids Res       Date:  2002-09-15       Impact factor: 16.971

8.  Complete DNA sequence and analysis of the transferable multiple-drug resistance plasmids (R Plasmids) from Photobacterium damselae subsp. piscicida isolates collected in Japan and the United States.

Authors:  Mi-Jung Kim; Ikuo Hirono; Ken Kurokawa; Takeshi Maki; John Hawke; Hidehiro Kondo; Mudjekeewis D Santos; Takashi Aoki
Journal:  Antimicrob Agents Chemother       Date:  2007-12-10       Impact factor: 5.191

9.  Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen.

Authors:  Takatsugu Goto; Atsushi Yamashita; Hideki Hirakawa; Minenosuke Matsutani; Kozo Todo; Kenshiro Ohshima; Hidehiro Toh; Kazuaki Miyamoto; Satoru Kuhara; Masahira Hattori; Tohru Shimizu; Shigeru Akimoto
Journal:  DNA Res       Date:  2008-02-07       Impact factor: 4.458

10.  Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus.

Authors:  Yoshinao Azuma; Akira Hosoyama; Minenosuke Matsutani; Naoko Furuya; Hiroshi Horikawa; Takeshi Harada; Hideki Hirakawa; Satoru Kuhara; Kazunobu Matsushita; Nobuyuki Fujita; Mutsunori Shirai
Journal:  Nucleic Acids Res       Date:  2009-07-28       Impact factor: 16.971
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