Tatajuba: exploring the distribution of homopolymer tracts.
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Authors
Bloomfield, Samuel
Stoakes, Emily
Grant, Andrew J
Page, Andrew J
Publication Date
2022-03Journal Title
NAR Genom Bioinform
ISSN
2631-9268
Publisher
Oxford University Press (OUP)
Volume
4
Issue
1
Language
eng
Type
Article
This Version
VoR
Metadata
Show full item recordCitation
de Oliveira Martins, L., Bloomfield, S., Stoakes, E., Grant, A. J., Page, A. J., & Mather, A. E. (2022). Tatajuba: exploring the distribution of homopolymer tracts.. NAR Genom Bioinform, 4 (1) https://doi.org/10.1093/nargab/lqac003
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.
Sponsorship
BBSRC (via Quadram Institute Bioscience) (BB/R012504/1)
Identifiers
PMC8808543, 35118377
External DOI: https://doi.org/10.1093/nargab/lqac003
This record's URL: https://www.repository.cam.ac.uk/handle/1810/334752
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