Show simple item record

dc.contributor.authorIraola, Gregorio [Univ Mayor, Ctr Biol Integrat, Santiago, Chile]es_CL
dc.contributor.authorFerres, Ignacioes_CL
dc.date.accessioned2020-04-08T14:11:55Z
dc.date.accessioned2020-04-13T18:12:49Z
dc.date.available2020-04-08T14:11:55Z
dc.date.available2020-04-13T18:12:49Z
dc.date.issued2018es_CL
dc.identifier.citationFerrés, I., & Iraola, G. (2018). MLSTar: automatic multilocus sequence typing of bacterial genomes in R. PeerJ, 6, e5098.es_CL
dc.identifier.issn2167-8359es_CL
dc.identifier.urihttps://doi.org/10.7717/peerj.5098es_CL
dc.identifier.urihttp://repositorio.umayor.cl/xmlui/handle/sibum/6233
dc.description.abstractMultilocus 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.es_CL
dc.description.sponsorshipAgencia Nacional de Investigacion e Innovacion of Uruguay [POS_NAC_1_2016_131079]es_CL
dc.description.sponsorshipThis work was supported by the Agencia Nacional de Investigacion e Innovacion of Uruguay post-graduation program (No. POS_NAC_1_2016_131079) granted to Ignacio Ferres. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.es_CL
dc.language.isoenes_CL
dc.publisherPEERJ INCes_CL
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Chile
dc.sourcePeerJ, JUN 2018. 6
dc.subjectMultidisciplinary Scienceses_CL
dc.titleMLSTar: automatic multilocus sequence typing of bacterial genomes in Res_CL
dc.typeArtículoes_CL
umayor.facultadCIENCIASes_CL
umayor.politicas.sherpa/romeoDOAJ Gold, Green Publishedes_CL
umayor.indexadoWOS:000435509800011es_CL
umayor.indexadoPMID: 29922519es_CL
dc.identifier.doiDOI: 10.7717/peerj.5098es_CL]
umayor.indicadores.wos-(cuartil)Q2es_CL
umayor.indicadores.scopus-(scimago-sjr)SCIMAGO/ INDICE H: 45 Hes_CL


Show simple item record