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MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity
Ikuo Uchiyama1, Toshio Higuchi, Mikihiko Kawai
1National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan. uchiyama@nibb.ac.jp
Nucleic Acids Research
|November 13, 2009
Summary
The Microbial Genome Database (MBGD) now offers advanced comparative genomics tools for microbial diversity research. Its enhanced features include improved functional annotation and the ability to analyze user-submitted genomes.
Area of Science:
- Microbial Genomics
- Bioinformatics
- Comparative Genomics
Background:
- The Microbial Genome Database (MBGD) is a key resource for microbial comparative genomics.
- It utilizes automated ortholog group identification for analyzing microbial genomes.
- The database currently houses nearly 1000 microbial genomes.
Purpose of the Study:
- To enhance MBGD as a comprehensive resource for microbial genome diversity investigation.
- To develop advanced functionalities for improved comparative genomic analysis.
- To expand the utility of MBGD for researchers in microbial genomics.
Main Methods:
- Implemented enhanced functional annotation with external database links for orthologous groups.
- Developed an interface for selecting genome comparison sets based on phenotypic properties.
- Integrated additional eukaryotic microbial genomes (fungi, protists) and higher eukaryotes as references.
- Enhanced the MyMBGD mode to accept raw genomic sequences for analysis, including a gene-finding procedure.
- Improved analysis functions, including ortholog identification with similar phylogenetic patterns.
Main Results:
- MBGD now provides more robust functional annotations and cross-database links.
- Users can now select genomes for comparison based on specific phenotypic traits.
- The inclusion of eukaryotic genomes broadens the scope of comparative analysis.
- The MyMBGD mode offers greater flexibility for users analyzing their own genomic data.
- Improved phylogenetic pattern analysis aids in understanding evolutionary relationships.
Conclusions:
- MBGD has been significantly upgraded with advanced functionalities for microbial comparative genomics.
- The enhanced database facilitates deeper insights into microbial genome diversity.
- MBGD serves as an increasingly valuable and versatile platform for genomic research.
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