Abstract
Comparative genomics is becoming an essential approach for identification of genes associated with a specific function or phenotype. Here, we introduce the microbial genome database for comparative analysis (MBGD), which is a comprehensive ortholog database among the microbial genomes available so far. MBGD contains several precomputed ortholog tables including the standard ortholog table covering the entire taxonomic range and taxon-specific ortholog tables for various major taxa. In addition, MBGD allows the users to create an ortholog table within any specified set of genomes through dynamic calculations. In particular, MBGD has a “My MBGD” mode where users can upload their original genome sequences and incorporate them into orthology analysis. The created ortholog table can serve as the basis for various comparative analyses. Here, we describe the use of MBGD and briefly explain how to utilize the orthology information during comparative genome analysis in combination with the stand-alone comparative genomics software RECOG, focusing on the application to comparison of closely related microbial genomes.
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Acknowledgment
The author thanks Hirokazu Chiba, Hiroyo Nishide, and Motohiro Mihara for the development and maintenance of the MBGD Web service. The development of MBGD is supported by National Bioscience Database Center, Japan Science Technology Agency. Computational resources were provided by the Data Integration and Analysis Facility, National Institute for Basic Biology.
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Uchiyama, I. (2017). Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG. In: Kihara, D. (eds) Protein Function Prediction. Methods in Molecular Biology, vol 1611. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7015-5_12
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DOI: https://doi.org/10.1007/978-1-4939-7015-5_12
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