ArticleNucleic acids research2019
MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Evolutionary signals in metabolic networks of insect endosymbionts revealed through comparative topological modeling.BMC genomics · 2026Article
- Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review.Frontiers in microbiology · 2026Review
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 2024Article
- The complete genome sequence of unculturableFrontiers in cellular and infection microbiology · 2024Article
- ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics.Nucleic acids research · 2023Article
- MADGAN:A microbe-disease association prediction model based on generative adversarial networks.Frontiers in microbiology · 2023Article
- Nitric Oxide Production and Effects in Group BPathogens (Basel, Switzerland) · 2022Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- Complete Genome Sequence of Ferrigenium kumadai An22, a Microaerophilic Iron-Oxidizing Bacterium Isolated from a Paddy Field Soil.Microbiology resource announcements · 2021Article
- Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).The Plant cell · 2021Article
- COG database update: focus on microbial diversity, model organisms, and widespread pathogens.Nucleic acids research · 2021Article
- GIMICA: host genetic and immune factors shaping human microbiota.Nucleic acids research · 2021Article
- Lipid Pathway Databases with a Focus on Algae.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes.PLoS pathogens · 2020Article
- The Quest for Orthologs benchmark service and consensus calls in 2020.Nucleic acids research · 2020Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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/.
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