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 Author | Felix Francis, Michael D. Dumas & Randall J. Wisser | |
| UD Author | Francis, Felix | en_US |
| UD Author | Dumas, Michael D. | en_US |
| UD Author | Wisser, Randall J. | en_US |
| Date Accessioned | 2018-08-06T15:21:32Z | |
| Date Available | 2018-08-06T15:21:32Z | |
| Copyright Date | Copyright © The Author(s) 2017 | en_US |
| Publication Date | 2017-03-16 | |
| Description | Publisher's PDF | en_US |
| Abstract | Isolating 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 |
| Department | University of Delaware. Center for Bioinformatics & Computational Biology. | en_US |
| Department | University of Delaware. Department of Plant and Soil Sciences. | en_US |
| Citation | Francis, 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 |
| DOI | 10.1038/srep44437 | en_US |
| ISSN | 2045-2322 | en_US |
| URL | http://udspace.udel.edu/handle/19716/23661 | |
| Language | en_US | en_US |
| Publisher | Nature Publishing Group | en_US |
| dc.rights | Article 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.rights | The 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.source | Scientific Reports | en_US |
| dc.source.uri | https://www.nature.com/srep/ | en_US |
| Title | ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing | en_US |
| Type | Article | en_US |
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