Tatajuba: exploring the distribution of homopolymer tracts.

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Authors
de Oliveira Martins, Leonardo  ORCID logo  https://orcid.org/0000-0001-5247-1320
Bloomfield, Samuel 
Stoakes, Emily 
Grant, Andrew J 
Page, Andrew J 
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.

Description

Acknowledgements: The authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC), and the two anonymous reviewers, who greatly improved the manuscript.

Keywords
31 Biological Sciences, 3102 Bioinformatics and Computational Biology, 3105 Genetics, Bioengineering, Genetics
Journal Title
NAR Genom Bioinform
Conference Name
Journal ISSN
2631-9268
2631-9268
Volume Title
4
Publisher
Oxford University Press (OUP)
Sponsorship
BBSRC (via Quadram Institute Bioscience) (BB/R012504/1)