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dc.contributor.author Clare, Amanda
dc.contributor.author Daykin, Jacqueline
dc.contributor.author Mills, Thomas
dc.contributor.author Zarges, Christine
dc.date.accessioned 2020-02-12T01:35:44Z
dc.date.available 2020-02-12T01:35:44Z
dc.date.issued 2019-07-13
dc.identifier.citation Clare , A , Daykin , J , Mills , T & Zarges , C 2019 , ' Evolutionary Search Techniques for the Lyndon Factorization of Biosequences ' Paper presented at Workshop on Evolutionary Computation for Permutation Problems at GECCO 2019 , Prague , Czech Republic , 13 Jul 2019 - 17 Jul 2019 , pp. 1543-1550 . en
dc.identifier.citation workshop en
dc.identifier.other PURE: 29426250
dc.identifier.other PURE UUID: dbaf7e1f-af84-4a4d-95b2-10d1e376a7c0
dc.identifier.other ORCID: /0000-0002-2829-4296/work/61185313
dc.identifier.other ORCID: /0000-0001-8315-3659/work/62636781
dc.identifier.other Scopus: 85070613742
dc.identifier.other handle.net: http://hdl.handle.net/2160/dbaf7e1f-af84-4a4d-95b2-10d1e376a7c0
dc.identifier.uri http://hdl.handle.net/2160/47117
dc.description.abstract A non-empty string x over an ordered alphabet is said to be a Lyndon word if it is alphabetically smaller than all of its cyclic rotations. Any string can be uniquely factored into Lyndon words and efficient algorithms exist to perform the factorization process in linear time and constant space. Lyndon words find wide-ranging applications including string matching and pattern inference in bioinformatics. Here we investigate the impact of permuting the alphabet ordering on the resulting factorization and demonstrate significant variations in the numbers of factors obtained. We also propose an evolutionary algorithm to find optimal orderings of the alphabet to enhance this factorization process and illustrate the impact of different operators. The flexibility of such an approach is illustrated by our use of five fitness functions which produce different factorizations suitable for different downstream tasks. en
dc.language.iso eng
dc.relation.ispartof en
dc.rights en
dc.subject algorithm en
dc.subject alphabet en
dc.subject artificial intelligence en
dc.subject Burrows-Wheeler Transform en
dc.subject factorization en
dc.subject evolutionary search en
dc.subject Genome en
dc.subject Lyndon word en
dc.subject pattern matching en
dc.subject string en
dc.subject word en
dc.title Evolutionary Search Techniques for the Lyndon Factorization of Biosequences en
dc.type /dk/atira/pure/researchoutput/researchoutputtypes/contributiontoconference/paper en
dc.description.version authorsversion en
dc.contributor.institution Department of Computer Science en
dc.description.status Peer reviewed en


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