Tatajuba: exploring the distribution of homopolymer tracts

de Oliveira Martins, Leonardo, Bloomfield, Samuel, Stoakes, Emily, Grant, Andrew J., Page, Andrew J. and Mather, Alison E. (2022) Tatajuba: exploring the distribution of homopolymer tracts. NAR Genomics and Bioinformatics, 4 (1). ISSN 2631-9268

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Abstract

Length 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.

Item Type: Article
Uncontrolled Keywords: genetics,structural biology,molecular biology,computer science applications,applied mathematics ,/dk/atira/pure/subjectarea/asjc/1300/1311
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Depositing User: LivePure Connector
Date Deposited: 30 Mar 2022 13:31
Last Modified: 19 Apr 2022 00:24
URI: https://ueaeprints.uea.ac.uk/id/eprint/84355
DOI: 10.1093/nargab/lqac003

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