MBGD: Microbial genome database for comparative analysis

Nucleic Acids Research

Volumn 31, Issue 1, 2003, Pages 58-62

  Uchiyama, Ikuo ^a  

^a National Institutes of Natural Sciences   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AUTOMATION; CLASSIFICATION; CONTROLLED STUDY; GENE ORDER; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; INFORMATION PROCESSING; MICROBIAL GENETICS; MICROBIAL GENOME DATABASE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TAXONOMY;

ALGORITHMS; ARCHAEA; BACTERIA; CLUSTER ANALYSIS; DATABASES, GENETIC; GENE ORDER; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOME, FUNGAL; PHYLOGENY; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA;

EID: 0037249403     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg109     Document Type: Review

References (20)

1. Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
2. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusava,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
3. Haft,D.H., Loftus,B.J., Richardson,D.L., Yang,F., Eisen,J.A., Paulsen,I.T. and White,O. (2001) TIGRFAMS: a protein family resource for the functional identification of proteins. Nucleic Acids Res., 29, 41-43.
4. Kanehisa,M., Goto,S., Kawashima,S. and Nakaya,A. (2002) The KEGG database at GenomeNet. Nucleic Acids Res., 30, 42-46.
5. Overbeek,R., Larsen,N., Pusch,G.D., D'Souza,M., Selkov,E.,Jr, Kyrpides,N., Fonstein,M., Maltsev,N. and Selkov,E. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res., 28, 123-125.
6. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., Rapp,B.A. and Wheeler,D.L. (2002) GenBank. Nucleic Acids Res., 30, 17-20.
7. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
8. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
9. Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
10. Falquet,L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J.A., Hofmann,K. and Bairoch,A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238.
11. Marchler-Bauer,A., Panchenko,A.R., Shoemaker,B.A., Thiessen,P.A., Geer,L.Y. and Bryant,S.H. (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283.
12. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L.L. (2002) The Pfam Protein Families Database. Nucleic Acids Res., 30, 276-280.
13. Letunic,I., Goodstadt,L., Dickens,N.J., Doerks,T., Schultz,J., Mott,R., Ciccarelli,F., Copley,R.R., Ponting,C.P. and Bork,P. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res., 30, 242-244.
14. Peterson,J.D., Umayam,L.A., Dickinson,T., Hickey,E.K. and White,O. (2001) The comprehensive microbial resource. Nucleic Acids Res., 29, 123-125.
15. Sneath,P.H.A. and Sokal,R.R. (1973) Numerical Taxonomy. Freeman, San Francisco.
16. Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 28, 10-14.
17. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1998) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
18. Huang,X. (1994) On global sequence alignment. Comput. Appl. Biosci., 10, 227-235.
19. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
20. Saitou,N. and Nei,M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.