ArticleNucleic acids research2010
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Natural History and Ecology of Interactions BetweenFrontiers in cellular and infection microbiology · 2022Article
- Contribution of a Novel Pertussis Toxin-Like Factor in Mediating Persistent Otitis Media.Frontiers in cellular and infection microbiology · 2022Article
- Identification of the Genes of the Plant PathogenFrontiers in microbiology · 2022Article
- Conservation of Ancient Genetic Pathways for Intracellular Persistence Among Animal Pathogenic Bordetellae.Frontiers in microbiology · 2019Article
- Strain-Specific Anti-inflammatory Properties of TwoFrontiers in cellular and infection microbiology · 2019Article
- Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing3 Biotech · 2018Article
- Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism in Carboxydothermus pertinax Revealed by Comparative Genome Analysis.Applied and environmental microbiology · 2018Article
- Toxin-positiveGut · 2018Article
- Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice.Microbiome · 2018Article
- TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci.Nucleic acids research · 2018Article
- Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374.Virulence · 2018Article
- Virulent Epidemic Pneumonia in Sheep Caused by the Human PathogenFrontiers in microbiology · 2018Article
- Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.Nucleic acids research · 2017Article
- Developing genome-reduced Pseudomonas chlororaphis strains for the production of secondary metabolites.BMC genomics · 2017Article
- Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism ofFrontiers in microbiology · 2017Article
- Article
- Comparative genomic analysis and phenazine production of Pseudomonas chlororaphis, a plant growth-promoting rhizobacterium.Genomics data · 2015Article
- The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.BMC genomics · 2015Article
- Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors.Scientific reports · 2015Article
- The plant growth-promoting bacteria Azospirillum amazonense: genomic versatility and phytohormone pathway.BioMed research international · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
mGenomeSubtractor performs an mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes for investigation of strain variable accessory regions. With parallel computing architecture, mGenomeSubtractor is able to run rapid BLAST searches of the segmented reference genome against multiple subject genomes at the DNA or amino acid level within a minute. In addition to comparison of protein coding sequences, the highly flexible sliding window-based genome fragmentation approach offered can be used to identify short unique sequences within or between genes. mGenomeSubtractor provides powerful schematic outputs for exploration of identified core and accessory regions, including searches against databases of mobile genetic elements, virulence factors or bacterial essential genes, examination of G+C content and binucleotide distribution bias, and integrated primer design tools. mGenomeSubtractor also allows for the ready definition of species-specific gene pools based on available genomes. Pan-genomic arrays can be easily developed using the efficient oligonucleotide design tool. This simple high-throughput in silico 'subtractive hybridization' analytical tool will support the rapidly escalating number of comparative bacterial genomics studies aimed at defining genomic biomarkers of evolutionary lineage, phenotype, pathotype, environmental adaptation and/or disease-association of diverse bacterial species. mGenomeSubtractor is freely available to all users without any login requirement at: http://bioinfo-mml.sjtu.edu.cn/mGS/.
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Registered trials
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.