ArticleNucleic acids research2015
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
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- Identifying protein function and functional links based on large-scale co-occurrence patterns.PloS one · 2022Article
- KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases.BMC bioinformatics · 2021Article
- The physiological potential of anammox bacteria as revealed by their core genome structure.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- OrthoDB in 2020: evolutionary and functional annotations of orthologs.Nucleic acids research · 2021Article
- Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes.Biomolecules · 2020Article
- Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.G3 (Bethesda, Md.) · 2020Article
- Long-term stability and Red Queen-like strain dynamics in marine viruses.Nature microbiology · 2020Article
- BioHackathon 2015: Semantics of data for life sciences and reproducible research.F1000Research · 2020Article
- Confronting Tigecycline-ResistantFrontiers in microbiology · 2020Article
- Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases.International journal of biological sciences · 2020Review
- An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms.Database : the journal of biological databases and curation · 2020Article
- Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types.Microbes and environments · 2020Article
- Biogenesis and functions of aminocarboxypropyluridine in tRNA.Nature communications · 2019Article
- Domainoid: domain-oriented orthology inference.BMC bioinformatics · 2019Article
- Biofilm-associated toxin and extracellular protease cooperatively suppress competitors in Bacillus subtilis biofilms.PLoS genetics · 2019Article
- Microbial genome analysis: the COG approach.Briefings in bioinformatics · 2019Review
- MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.Nucleic acids research · 2019Article
- OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.Nucleic acids research · 2019Article
- Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method.PloS one · 2019Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.