UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks.

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. Green open access

[thumbnail of Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks..pdf]
Preview
PDF
Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks..pdf
Available under License : See the attached licence file.

Download (400kB)

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.ucl.ac.uk/id/eprint/1469805
Downloads since deposit
157Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item