title: An automated system for genome analysis to support microbial whole-genome shotgun sequencing.
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.
authors.affiliation: Deep-sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka, Kanagawa.
authors.forename: T
authors.initials: T
authors.lastname: Sakiyama
authors.forename: H
authors.initials: H
authors.lastname: Takami
authors.forename: N
authors.initials: N
authors.lastname: Ogasawara
authors.forename: S
authors.initials: S
authors.lastname: Kuhara
authors.forename: T
authors.initials: T
authors.lastname: Kozuki
authors.forename: K
authors.initials: K
authors.lastname: Doga
authors.forename: A
authors.initials: A
authors.lastname: Ohyama
authors.forename: K
authors.initials: K
authors.lastname: Horikoshi
mesh_terms: D001331:Automation; D001407:Bacillus / Q000235:genetics*; D001330:Electronic Data Processing / Q000379:methods; D016680:Genome, Bacterial; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software