Literature DB >> 11752256

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.

Masaki Fumoto1, Satoru Miyazaki, Hideaki Sugawara.   

Abstract

Genome Information Broker (GIB) is a powerful tool for the study of comparative genomics. GIB allows users to retrieve and display partial and/or whole genome sequences together with the relevant biological annotation. GIB has accumulated all the completed microbial genome and has recently been expanded to include Arabidopsis thaliana genome data from DDBJ/EMBL/GenBank. In the near future, hundreds of genome sequences will be determined. In order to handle such huge data, we have enhanced the GIB architecture by using XML, CORBA and distributed RDBs. We introduce the new GIB here. GIB is freely accessible at http://gib.genes.nig.ac.jp/.

Entities:  

Mesh：

Year:  2002        PMID： 11752256      PMCID： PMC99149          DOI： 10.1093/nar/30.1.66

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  5 in total

1.  Genome Information Broker for large and small genomes.

Authors:  T Tamura; H Mori; H Sugawara
Journal:  Trends Genet       Date:  1997-12       Impact factor: 11.639

Review 2.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

3.  Improved tools for biological sequence comparison.

Authors:  W R Pearson; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1988-04       Impact factor: 11.205

4.  Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.

Authors:  C M Fraser; S Casjens; W M Huang; G G Sutton; R Clayton; R Lathigra; O White; K A Ketchum; R Dodson; E K Hickey; M Gwinn; B Dougherty; J F Tomb; R D Fleischmann; D Richardson; J Peterson; A R Kerlavage; J Quackenbush; S Salzberg; M Hanson; R van Vugt; N Palmer; M D Adams; J Gocayne; J Weidman; T Utterback; L Watthey; L McDonald; P Artiach; C Bowman; S Garland; C Fuji; M D Cotton; K Horst; K Roberts; B Hatch; H O Smith; J C Venter
Journal:  Nature       Date:  1997-12-11       Impact factor: 49.962

5.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

Authors:  R D Fleischmann; M D Adams; O White; R A Clayton; E F Kirkness; A R Kerlavage; C J Bult; J F Tomb; B A Dougherty; J M Merrick
Journal:  Science       Date:  1995-07-28       Impact factor: 47.728
  5 in total
  15 in total

1.  3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.

Authors:  Keiran Fleming; Arne Müller; Robert M MacCallum; Michael J E Sternberg
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  DNA Data Bank of Japan (DDBJ) in XML.

Authors:  S Miyazaki; H Sugawara; T Gojobori; Y Tateno
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

3.  Biological SOAP servers and web services provided by the public sequence data bank.

Authors:  H Sugawara; S Miyazaki
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

4.  Whole-genome microarray and gene deletion studies reveal regulation of the polyhydroxyalkanoate production cycle by the stringent response in Ralstonia eutropha H16.

Authors:  Christopher J Brigham; Daan R Speth; ChoKyun Rha; Anthony J Sinskey
Journal:  Appl Environ Microbiol       Date:  2012-09-07       Impact factor: 4.792

5.  Strategies and tools for whole-genome alignments.

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Journal:  Genome Res       Date:  2003-01       Impact factor: 9.043

6.  DDBJ progress report.

Authors:  Eli Kaminuma; Takehide Kosuge; Yuichi Kodama; Hideo Aono; Jun Mashima; Takashi Gojobori; Hideaki Sugawara; Osamu Ogasawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2010-11-09       Impact factor: 16.971

7.  The MetJ regulon in gammaproteobacteria determined by comparative genomics methods.

Authors:  Anne M Augustus; Leonard D Spicer
Journal:  BMC Genomics       Date:  2011-11-14       Impact factor: 3.969

8.  DDBJ in preparation for overview of research activities behind data submissions.

Authors:  Kousaku Okubo; Hideaki Sugawara; Takashi Gojobori; Yoshio Tateno
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

9.  Evaluation of three automated genome annotations for Halorhabdus utahensis.

Authors:  Peter Bakke; Nick Carney; Will Deloache; Mary Gearing; Kjeld Ingvorsen; Matt Lotz; Jay McNair; Pallavi Penumetcha; Samantha Simpson; Laura Voss; Max Win; Laurie J Heyer; A Malcolm Campbell
Journal:  PLoS One       Date:  2009-07-20       Impact factor: 3.240

10.  DDBJ launches a new archive database with analytical tools for next-generation sequence data.

Authors:  Eli Kaminuma; Jun Mashima; Yuichi Kodama; Takashi Gojobori; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura
Journal:  Nucleic Acids Res       Date:  2009-10-22       Impact factor: 16.971
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