Word entropy-based approach to detect highly variable genetic markers for bacterial genotyping

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dc.contributor.authorNykrýnová, Markétacs
dc.contributor.authorBartoň, Vojtěchcs
dc.contributor.authorSedlář, Karelcs
dc.contributor.authorBezdíček, Matějcs
dc.contributor.authorLengerová, Martinacs
dc.contributor.authorŠkutková, Helenacs
dc.coverage.issue1cs
dc.coverage.volume12cs
dc.date.accessioned2021-02-25T11:54:36Z
dc.date.available2021-02-25T11:54:36Z
dc.date.issued2021-02-03cs
dc.description.abstractGenotyping methods are used to distinguish bacterial strains from one species. Thus, distinguishing bacterial strains on a global scale, between countries or local districts in one country is possible. However, the highly selected bacterial populations (e.g. local populations in hospital) are typically closely related and low diversified. Therefore, currently used typing methods are not able to distinguish individual strains from each other. Here, we present a novel pipeline to detect highly variable genetic segments for genotyping a closely related bacterial population. The method is based on a degree of disorder in analyzed sequences that can be represented by sequence entropy. With the identified variable sequences, it is possible to find out transmission routes and sources of highly virulent and multiresistant strains. The proposed method can be used for any bacterial population, and due to its whole genome range, also noncoding regions are examined.en
dc.formattextcs
dc.format.extent1-8cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationFrontiers in Microbiology. 2021, vol. 12, issue 1, p. 1-8.en
dc.identifier.doi10.3389/fmicb.2021.631605cs
dc.identifier.issn1664-302Xcs
dc.identifier.other167886cs
dc.identifier.urihttp://hdl.handle.net/11012/196358
dc.language.isoencs
dc.publisherFrontiers Media SAcs
dc.relation.ispartofFrontiers in Microbiologycs
dc.relation.urihttps://www.frontiersin.org/articles/10.3389/fmicb.2021.631605/fullcs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/1664-302X/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectgenotypingen
dc.subjectentropyen
dc.subjectgenetic markersen
dc.subjectclosely related bacteriaen
dc.subjectMLSTen
dc.titleWord entropy-based approach to detect highly variable genetic markers for bacterial genotypingen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-167886en
sync.item.dbtypeVAVen
sync.item.insts2021.03.01 16:54:08en
sync.item.modts2021.03.01 16:14:09en
thesis.grantorVysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií. Ústav biomedicínského inženýrstvícs
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