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. 2007 Jan;35(Database issue):D343-6.
doi: 10.1093/nar/gkl978. Epub 2006 Nov 29.

MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups

Ikuo Uchiyama  1
Affiliations

MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups

Ikuo Uchiyama. Nucleic Acids Res. 2007 Jan.

Abstract

The microbial genome database for comparative analysis (MBGD) is a comprehensive platform for microbial comparative genomics. The central function of MBGD is to create orthologous groups among multiple genomes from precomputed all-against-all similarity relationships using the DomClust algorithm. The database now contains >300 published genomes and the number continues to grow. For researchers who are interested in ongoing genome projects, we have now started a new service called 'My MBGD,' which allows users to add their own genome sequences to MBGD for the purpose of identifying orthologs among both the new and the existing genomes. Furthermore, in order to make available the rapidly accumulating information on closely related genome sequences, we enhanced the interface for pairwise genome comparisons using the CGAT interface, which allows users to see nucleotide sequence alignments of non-coding as well as coding regions. MBGD is available at http://mbgd.genome.ad.jp/.

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Figures

Figure 1
Figure 1
Increase in the number of complete microbial (bacteria and archaea) genome sequences. The number of genomes published between January and June 2006 was doubled for the purpose of estimating total number of genomes newly determined during the year 2006. The data are taken from the GOLD database (13).
Figure 2
Figure 2
The user interface flow diagram of MBGD. The arrows represent possible transitions between pages. The new functionalities, My MBGD and CGAT AlignmentViewer, are highlighted.
Figure 3
Figure 3
The protocol for database construction in MBGD.
Figure 4
Figure 4
The CGAT interface showing the nucleotide sequence alignment between the genomes of two strains of Escherichia coli, 536 (‘ug1’) and K-12 (‘eco’). Here, the 536 genome is registered via the My MBGD functionality.
See this image and copyright information in PMC

References

    1. Uchiyama I. MBGD: microbial genome database for comparative analysis. Nucleic Acids Res. 2003;31:58–62. - PMC - PubMed
    1. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4:41. - PMC - PubMed
    1. Haft D.H., Loftus B.J., Richardson D.L., Yang F., Eisen J.A., Paulsen I.T., White O. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 2001;29:41–43. - PMC - PubMed
    1. Chen F., Mackey A.J., Stoeckert C.J., Jr, Roos D.S. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 2006;34:D363–D368. - PMC - PubMed
    1. Markowitz V.M., Korzeniewski F., Palaniappan K., Szeto E., Werner G., Padki A., Zhao X., Dubchak I., Hugenholtz P., Anderson I., et al. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 2006;34:D344–D348. - PMC - PubMed

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