An algorithm for mapping short reads to a dynamically changing genomic sequence

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dc.contributor.author Iliopoulos, Costas S.
dc.contributor.author Kourie, Derrick G.
dc.contributor.author Mouchard, Laurent
dc.contributor.author Musombuka, Themba K.
dc.contributor.author Pissis, Solon P.
dc.contributor.author De Ridder, Corne
dc.date.accessioned 2017-01-10T08:25:51Z
dc.date.available 2017-01-10T08:25:51Z
dc.date.issued 2012-01
dc.description.abstract Next-generation sequencing technologies have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible. Due to the dramatic increase in the amount of data generated, a challenging task is to map (align) a set of reads to a reference genome. In this paper, we study a different version of this problem: mapping these reads to a dynamically changing genomic sequence. We propose a new practical algorithm, which employs a suitable data structure that takes into account potential dynamic effects (replacements, insertions, deletions) on the genomic sequence. The presented experimental results demonstrate that the proposed approach can be extended and applied to address the problem of mapping short reads to multiple related genomes. en_ZA
dc.description.department Computer Science en_ZA
dc.description.librarian hb2016 en_ZA
dc.description.uri http://www.elsevier.com/locate/jda en_ZA
dc.identifier.citation Iliopoulos, CS, Kourie, D, Mouchard, L, Musombuka, TK, Pissis, SP & De Ridder, C 2012, 'An algorithm for mapping short reads to a dynamically changing genomic sequence', Journal of Discrete Algorithms, vol. 10, no. 1, pp. 15-22. en_ZA
dc.identifier.issn 1570-8667 (print)
dc.identifier.issn 1570-8675 (online)
dc.identifier.other 10.1016/j.jda.2011.08.006
dc.identifier.uri http://hdl.handle.net/2263/58460
dc.language.iso en en_ZA
dc.publisher Elsevier en_ZA
dc.rights © 2011 Elsevier B.V. All rights reserved. This is an open access article under an Elsevier user license. en_ZA
dc.subject String algorithms en_ZA
dc.subject Next-generation sequencing en_ZA
dc.subject Mapping en_ZA
dc.title An algorithm for mapping short reads to a dynamically changing genomic sequence en_ZA
dc.type Article en_ZA


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