ArticlePeerJ2018
MLSTar: automatic multilocus sequence typing of bacterial genomes in R.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Novel multidrug-resistant sublineages ofmSphere · 2023Article
- Article
- Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.Microbiome · 2022Article
- Genomic Characterization and Antimicrobial Susceptibility of Dromedary-AssociatedApplied and environmental microbiology · 2022Article
- In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.BMC genomics · 2022Article
- SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels.BMC genomics · 2021Article
- Investigating the Meat Pathway as a Source of Human Nontyphoidal Salmonella Bloodstream Infections and Diarrhea in East Africa.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
- Pangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts.Scientific reports · 2021Article
- Genotypic and Phenotypic Characterization ofToxins · 2021Observational
- FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies.Bioinformatics and biology insights · 2021Article
- Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications.Wellcome open research · 2018Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes. The PubMLST database is the most comprehensive resource of described schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows us to (i) connect with the PubMLST database to select a target scheme, (ii) screen a desired set of genomes to assign alleles and sequence types, and (iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze more than 2,500 bacterial genomes from different species, showing great accuracy, and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.
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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.