ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing

Author(s)Francis, Felix
Author(s)Dumas, Michael D.
Author(s)Wisser, Randall J.
Ordered AuthorFelix Francis, Michael D. Dumas & Randall J. Wisser
UD AuthorFrancis, Felixen_US
UD AuthorDumas, Michael D.en_US
UD AuthorWisser, Randall J.en_US
Date Accessioned2018-08-06T15:21:32Z
Date Available2018-08-06T15:21:32Z
Copyright DateCopyright © The Author(s) 2017en_US
Publication Date2017-03-16
DescriptionPublisher's PDFen_US
AbstractIsolating and sequencing specific regions in a genome is a cornerstone of molecular biology. This has been facilitated by computationally encoding the thermodynamics of DNA hybridization for automated design of hybridization and priming oligonucleotides. However, the repetitive composition of genomes challenges the identification of target-specific oligonucleotides, which limits genetics and genomics research on many species. Here, a tool called ThermoAlign was developed that ensures the design of target-specific primer pairs for DNA amplification. This is achieved by evaluating the thermodynamics of hybridization for full-length oligonucleotide-template alignments — thermoalignments — across the genome to identify primers predicted to bind specifically to the target site. For amplificationbased resequencing of regions that cannot be amplified by a single primer pair, a directed graph analysis method is used to identify minimum amplicon tiling paths. Laboratory validation by standard and long-range polymerase chain reaction and amplicon resequencing with maize, one of the most repetitive genomes sequenced to date (≈85% repeat content), demonstrated the specificity-by-design functionality of ThermoAlign. ThermoAlign is released under an open source license and bundled in a dependency-free container for wide distribution. It is anticipated that this tool will facilitate multiple applications in genetics and genomics and be useful in the workflow of high-throughput targeted resequencing studies.en_US
DepartmentUniversity of Delaware. Center for Bioinformatics & Computational Biology.en_US
DepartmentUniversity of Delaware. Department of Plant and Soil Sciences.en_US
CitationFrancis, F. et al. ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing. Sci. Rep. 7, 44437; doi: 10.1038/srep44437 (2017).en_US
PublisherNature Publishing Groupen_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.rightsThe article for which you have requested permission has been distributed under a Creative Commons CC-BY license (please see the article itself for the license version number). You may reuse this material without obtaining permission from Nature Publishing Group, providing that the author and the original source of publication are fully acknowledged, as per the terms of the license.en_US
dc.sourceScientific Reportsen_US
TitleThermoAlign: a genome-aware primer design tool for tiled amplicon resequencingen_US
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