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dc.contributor.authorde Oliveira Martins, Leonardo
dc.contributor.authorBloomfield, Samuel
dc.contributor.authorStoakes, Emily
dc.contributor.authorGrant, Andrew J
dc.contributor.authorPage, Andrew J
dc.contributor.authorMather, Alison E
dc.date.accessioned2022-03-08T02:03:22Z
dc.date.available2022-03-08T02:03:22Z
dc.date.issued2022-03
dc.identifier.issn2631-9268
dc.identifier.otherPMC8808543
dc.identifier.other35118377
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/334752
dc.description.abstractLength variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and help predict their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source licence GNU GPLv3.
dc.languageeng
dc.publisherOxford University Press (OUP)
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourcenlmid: 101756213
dc.sourceessn: 2631-9268
dc.titleTatajuba: exploring the distribution of homopolymer tracts.
dc.typeArticle
dc.date.updated2022-03-08T02:03:21Z
prism.issueIdentifier1
prism.publicationNameNAR Genom Bioinform
prism.volume4
dc.identifier.doi10.17863/CAM.82182
dcterms.dateAccepted2022-01-05
rioxxterms.versionofrecord10.1093/nargab/lqac003
rioxxterms.versionVoR
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidde Oliveira Martins, Leonardo [0000-0001-5247-1320]
dc.contributor.orcidMather, Alison E [0000-0001-6513-3515]
dc.identifier.eissn2631-9268
pubs.funder-project-idBBSRC (via Quadram Institute Bioscience) (BB/R012504/1)
cam.issuedOnline2022-02-02


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International