Langdon, WB;
(2015)
Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks.
BioData Min
, 8
(1)
, Article 1. 10.1186/s13040-014-0034-0.
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Abstract
Genetic studies are increasingly based on short noisy next generation scanners. Typically complete DNA sequences are assembled by matching short NextGen sequences against reference genomes. Despite considerable algorithmic gains since the turn of the millennium, matching both single ended and paired end strings to a reference remains computationally demanding. Further tailoring Bioinformatics tools to each new task or scanner remains highly skilled and labour intensive. With this in mind, we recently demonstrated a genetic programming based automated technique which generated a version of the state-of-the-art alignment tool Bowtie2 which was considerably faster on short sequences produced by a scanner at the Broad Institute and released as part of The Thousand Genome Project.
| Type: | Article |
|---|---|
| Title: | Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1186/s13040-014-0034-0 |
| Publisher version: | http://dx.doi.org/10.1186/s13040-014-0034-0 |
| Language: | English |
| Additional information: | © 2015 Langdon; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
| Keywords: | Double-ended DNA sequence, High throughput Solexa 454 nextgen NGS sequence query, Homo sapiens genome reference consortium HG19, Rapid fuzzy string matching |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/1469805 |
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