Uchiyama Ikuo
Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
Methods Mol Biol. 2017;1611:147-168. doi: 10.1007/978-1-4939-7015-5_12.
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.
比较基因组学正成为鉴定与特定功能或表型相关基因的重要方法。在此，我们介绍用于比较分析的微生物基因组数据库（MBGD），它是目前可用的微生物基因组之间的一个综合直系同源数据库。MBGD包含几个预先计算好的直系同源表，包括覆盖整个分类范围的标准直系同源表以及针对各种主要分类群的分类群特异性直系同源表。此外，MBGD允许用户通过动态计算在任何指定的基因组集合内创建直系同源表。特别是，MBGD有一个“我的MBGD”模式，用户可以上传他们的原始基因组序列并将其纳入直系同源分析。创建的直系同源表可作为各种比较分析的基础。在此，我们描述MBGD的使用，并简要解释如何在比较基因组分析过程中结合独立的比较基因组学软件RECOG利用直系同源信息，重点是其在密切相关微生物基因组比较中的应用。
