Database Commons

a catalog of worldwide biological databases

Microbial Genome Database for Comparative Analysis (MBGD) is a comprehensive ortholog database encompassing published complete microbial genomes. The ortholog tables in MBGD are constructed in a hierarchical manner. The top-level ortholog table is now constructed from 1,812 genus-level pan-genomes, 6,268 species-level pan-genomes, and 34,079 genomes in total. To support analyses of newly sequenced genomes, MBGD updates MyMBGD functionality, which offers two analysis modes: assignment mode and clustering mode. Assignment mode rapidly classifies genes in the query genomes into existing MBGD ortholog groups, while clustering mode performs de novo clustering of query genomes using the DomClust program. In assignment mode, users can evaluate the presence of genomic functions, as defined in the KEGG Module database, in each query genome using the Genomaple software and compare the results across multiple genomes. To enhance this analysis, we developed a method to subdivide MBGD ortholog groups as needed to improve cross-references to the KEGG Orthology groups. Another notable feature is the phylogenetic profile search interface, which enables users to specify a set of organisms in which orthologs are present or absent (i.e., a phylogenetic profile), and search for ortholog groups with similar phylogenetic profiles. To construct a phylogenetic profile, users can search organisms by specifying phenotype, environment, taxonomy, or a particular ortholog group. MBGD is available at https://mbgd.nibb.ac.jp/.

The Microbial Genome Database for Comparative Analysis (MBGD) is a database for comparative genomics based on comprehensive orthology analysis of bacteria, archaea and unicellular eukaryotes. MBGD now contains 6318 genomes. To utilize the database for both closely related and distantly related genomes, MBGD previously provided two types of ortholog tables: the standard ortholog table containing one representative genome from each genus covering the entire taxonomic range and the taxon specific ortholog tables for each taxon. However, this approach has a drawback in that the standard ortholog table contains only genes that are conserved in the representative genomes. To address this problem, we developed a stepwise procedure to construct ortholog tables hierarchically in a bottom-up manner. By using this approach, the new standard ortholog table now covers the entire gene repertoire stored in MBGD. In addition, we have enhanced several functionalities, including rapid and flexible keyword searching, profile-based sequence searching for orthology assignment to a user query sequence, and displaying a phylogenetic tree of each taxon based on the concatenated core gene sequences. For integrative database searching, the core data in MBGD are represented in Resource Description Framework (RDF) and a SPARQL interface is provided to search them. MBGD is available at http://mbgd.genome.ad.jp/.

The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

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/.

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/.

MBGD is a workbench system for comparative analysis of completely sequenced microbial genomes. The central function of MBGD is to create an orthologous gene classification table using precomputed all-against-all similarity relationships among genes in multiple genomes. In MBGD, an automated classification algorithm has been implemented so that users can create their own classification table by specifying a set of organisms and parameters. This feature is especially useful when the user's interest is focused on some taxonomically related organisms. The created classification table is stored into the database and can be explored combining with the data of individual genomes as well as similarity relationships among genomes. Using these data, users can carry out comparative analyses from various points of view, such as phylogenetic pattern analysis, gene order comparison and detailed gene structure comparison. MBGD is accessible at http://mbgd.genome.ad.jp/.