A metaheuristic approach for the sequencing by hybridization problem with positive and negative errors

Nikolakopoulos, A; Sarimveis, H

dc.contributor.author	Nikolakopoulos, A	en
dc.contributor.author	Sarimveis, H	en
dc.date.accessioned	2014-03-01T01:27:42Z
dc.date.available	2014-03-01T01:27:42Z
dc.date.issued	2008	en
dc.identifier.issn	0952-1976	en
dc.identifier.uri	https://dspace.lib.ntua.gr/xmlui/handle/123456789/18545
dc.subject	DNA sequencing with errors	en
dc.subject	Metaheuristics	en
dc.subject	Sequencing by hybridization	en
dc.subject	Traveling salesman problem	en
dc.subject.classification	Automation & Control Systems	en
dc.subject.classification	Computer Science, Artificial Intelligence	en
dc.subject.classification	Engineering, Multidisciplinary	en
dc.subject.classification	Engineering, Electrical & Electronic	en
dc.subject.other	DNA sequences	en
dc.subject.other	Error analysis	en
dc.subject.other	Problem solving	en
dc.subject.other	Traveling salesman problem	en
dc.subject.other	DNA sequencing with errors	en
dc.subject.other	Metaheuristics	en
dc.subject.other	Sequencing by hybridization	en
dc.subject.other	Heuristic methods	en
dc.title	A metaheuristic approach for the sequencing by hybridization problem with positive and negative errors	en
heal.type	journalArticle	en
heal.identifier.primary	10.1016/j.engappai.2007.03.004	en
heal.identifier.secondary	http://dx.doi.org/10.1016/j.engappai.2007.03.004	en
heal.language	English	en
heal.publicationDate	2008	en
heal.abstract	This work introduces a metaheuristic method for the reconstruction of the DNA string from its l-mer content in the presence oflarge amounts of positive and negative errors. The procedure consists of three parts: the formulation of the problem as an asymmetric traveling salesman problem (ATSP), a technique for handling the positive errors and an optimization algorithm that solves the formulated problem. The optimization algorithm is a variation of the threshold accepting method with intense local search and its function is controlled by a size diminishing shell. The optimization algorithm is used consecutively on ATSPs of continuously decreasing sizes till it reaches a final solution. The proposed method provides solutions of better quality compared to algorithms in the recent bibliography. (c) 2007 Elsevier Ltd. All rights reserved.	en
heal.publisher	PERGAMON-ELSEVIER SCIENCE LTD	en
heal.journalName	Engineering Applications of Artificial Intelligence	en
dc.identifier.doi	10.1016/j.engappai.2007.03.004	en
dc.identifier.isi	ISI:000255316600009	en
dc.identifier.volume	21	en
dc.identifier.issue	2	en
dc.identifier.spage	247	en
dc.identifier.epage	258	en