MBGD update 2010: Toward a comprehensive resource for exploring microbial genome diversity

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Uchiyama, Ikuo ^a   Higuchi, Toshio ^b   Kawai, Mikihiko ^a  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^b INTEC Systems Institute Inc   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; COMPUTER INTERFACE; FUNGAL GENOME; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; INTERNET; MICROBIAL GENETICS; MICROBIAL GENOME DATABASE; MOLECULAR PHYLOGENY; NONHUMAN; ORTHOLOGY; PHENOTYPE; PRIORITY JOURNAL; PROTOZOAL GENETICS; ANIMAL; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; GENOMICS; HUMAN; INFORMATION RETRIEVAL; METHODOLOGY; NUCLEIC ACID DATABASE; PHYLOGENY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

EUKARYOTA; FUNGI; PROTISTA;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; GENOME, BACTERIAL; GENOME, FUNGAL; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 75549085348     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp948     Document Type: Article

References (15)

1. Uchiyama, I. (2003) MBGD: microbial genome database for comparative analysis. Nucleic Acids Res., 31, 58-62.
2. Uchiyama, I. (2007) MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res., 35, D343-D346.
3. Uchiyama, I. (2006) Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res., 34, 647-658.
4. 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.
5. Alm, E.J., Huang, K.H., Price, M.N., Koche, R.P., Keller, K., Dubchak, I.L. and Arkin, A.P. (2005) The MicrobesOnline Web site for comparative genomics. Genome Res., 15, 1015-1022.
6. Markowitz, V.M., Szeto, E., Palaniappan, K., Grechkin, Y., Chu, K., Chen, I.M., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K. et al. (2008) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res., 36, D528-D533.
7. Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P. (2008) eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res., 36, D250-D254.
8. Schneider, A., Dessimoz, C. and Gonnet, G.H. (2007) OMA Browser-exploring orthologous relations across 352 complete genomes. Bioinformatics, 23, 2180-2182.
9. Wu, J., Kasif, S. and DeLisi, C. (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics, 19, 1524-1530.
10. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. and Yeates, T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
11. Enault, F., Suhre, K. and Claverie, J.M. (2005) Phydbac 'Gene Function Predictor': a gene annotation tool based on genomic context analysis. BMC Bioinformatics, 6, 247.
12. Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A., Simonovic, M. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
13. Liolios, K., Mavromatis, K., Tavernarakis, N. and Kyrpides, N.C. (2008) The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res., 36, D475-D479.
14. Besemer, J., Lomsadze, A. and Borodovsky, M. (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res., 29, 2607-2618.
15. Delcher, A.L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.