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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp948
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

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

Ikuo Uchiyama1,*, Toshio Higuchi2 and Mikihiko Kawai1

1National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan and 2Intec Systems Institute, Inc., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-0075, Japan

*To whom correspondence should be addressed. Tel: +81 564 55 7629; Fax: +81 564 55 7625; Email: uchiyama{at}nibb.ac.jp

Received September 14, 2009. Revised October 9, 2009. Accepted October 12, 2009.

The microbial genome database (MBGD) for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature of MBGD is that it allows users to create ortholog groups using a specified subgroup of organisms. The database is constantly updated and now contains almost 1000 genomes. To utilize the MBGD database as a comprehensive resource for investigating microbial genome diversity, we have developed the following advanced functionalities: (i) enhanced assignment of functional annotation, including external database links to each orthologous group, (ii) interface for choosing a set of genomes to compare based on phenotypic properties, (iii) the addition of more eukaryotic microbial genomes (fungi and protists) and some higher eukaryotes as references and (iv) enhancement of the MyMBGD mode, which allows users to add their own genomes to MBGD and now accepts raw genomic sequences without any annotation (in such a case, it runs a gene-finding procedure before identifying the orthologs). Some analysis functions, such as the function to find orthologs with similar phylogenetic patterns, have also been improved. MBGD is accessible at http://mbgd.genome.ad.jp/.


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