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Literature DB >> 12519947

MBGD: microbial genome database for comparative analysis.

Abstract

MBGD is a workbench system for comparative analysis of completely sequenced microbial genomes. The central function of MBGD is to create an orthologous gene classification table using precomputed all-against-all similarity relationships among genes in multiple genomes. In MBGD, an automated classification algorithm has been implemented so that users can create their own classification table by specifying a set of organisms and parameters. This feature is especially useful when the user's interest is focused on some taxonomically related organisms. The created classification table is stored into the database and can be explored combining with the data of individual genomes as well as similarity relationships among genomes. Using these data, users can carry out comparative analyses from various points of view, such as phylogenetic pattern analysis, gene order comparison and detailed gene structure comparison. MBGD is accessible at http://mbgd.genome.ad.jp/.

Mesh：

Year: 2003 PMID： 12519947 PMCID： PMC165556 DOI： 10.1093/nar/gkg109

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

20 in total

1. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.

Authors: R Overbeek; N Larsen; G D Pusch; M D'Souza; E Selkov; N Kyrpides; M Fonstein; N Maltsev; E Selkov
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. The Comprehensive Microbial Resource.

Authors: J D Peterson; L A Umayam; T Dickinson; E K Hickey; O White
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

3. TIGRFAMs: a protein family resource for the functional identification of proteins.

Authors: D H Haft; B J Loftus; D L Richardson; F Yang; J A Eisen; I T Paulsen; O White
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

4. Who's your neighbor? New computational approaches for functional genomics.

Authors: M Y Galperin; E V Koonin
Journal: Nat Biotechnol Date: 2000-06 Impact factor: 54.908

5. GenBank.

Authors: Dennis A Benson; Ilene Karsch-Mizrachi; David J Lipman; James Ostell; Barbara A Rapp; David L Wheeler
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

6. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.

Authors: M Pellegrini; E M Marcotte; M J Thompson; D Eisenberg; T O Yeates
Journal: Proc Natl Acad Sci U S A Date: 1999-04-13 Impact factor: 11.205

7. Database resources of the National Center for Biotechnology Information.

Authors: D L Wheeler; C Chappey; A E Lash; D D Leipe; T L Madden; G D Schuler; T A Tatusova; B A Rapp
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

Review 8. 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

9. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors: J D Thompson; D G Higgins; T J Gibson
Journal: Nucleic Acids Res Date: 1994-11-11 Impact factor: 16.971

10. The COG database: new developments in phylogenetic classification of proteins from complete genomes.

Authors: R L Tatusov; D A Natale; I V Garkavtsev; T A Tatusova; U T Shankavaram; B S Rao; B Kiryutin; M Y Galperin; N D Fedorova; E V Koonin
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

52 in total

1. Direct and indirect regulation of the ycnKJI operon involved in copper uptake through two transcriptional repressors, YcnK and CsoR, in Bacillus subtilis.

Authors: Kazutake Hirooka; Takayosh Edahiro; Kosuke Kimura; Yasutaro Fujita
Journal: J Bacteriol Date: 2012-08-17 Impact factor: 3.490

2. Regulation of the rhaEWRBMA Operon Involved in l-Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis.

Authors: Kazutake Hirooka; Yusuke Kodoi; Takenori Satomura; Yasutaro Fujita
Journal: J Bacteriol Date: 2015-12-28 Impact factor: 3.490

3. Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus.

Authors: Hideto Takami; Yoshihiro Takaki; Gab-Joo Chee; Shinro Nishi; Shigeru Shimamura; Hiroko Suzuki; Satomi Matsui; Ikuo Uchiyama
Journal: Nucleic Acids Res Date: 2004-12-01 Impact factor: 16.971

4. Disruption of tetR type regulator adeN by mobile genetic element confers elevated virulence in Acinetobacter baumannii.

Authors: Rajagopalan Saranathan; Sudhakar Pagal; Ajit R Sawant; Archana Tomar; M Madhangi; Suresh Sah; Annapurna Satti; K P Arunkumar; K Prashanth
Journal: Virulence Date: 2017-04-24 Impact factor: 5.882

5. MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

Authors: Ikuo Uchiyama; Toshio Higuchi; Mikihiko Kawai
Journal: Nucleic Acids Res Date: 2009-11-11 Impact factor: 16.971

6. Elucidating genome structure evolution by analysis of isoapostatic gene clusters using statistics of variance of gene distances.

Authors: Naobumi V Sasaki; Naoki Sato
Journal: Genome Biol Evol Date: 2009-12-18 Impact factor: 3.416

7. Development and application of a dapB-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium Pseudomonas stutzeri A15.

Authors: Hans Rediers; Victoria Bonnecarrère; Paul B Rainey; Kelly Hamonts; Jos Vanderleyden; René De Mot
Journal: Appl Environ Microbiol Date: 2003-11 Impact factor: 4.792