Iterated Local Search for de Novo Genomic Sequencing

Dorronsoro, Bernabé; Bouvry, Pascal; Alba, Enrique

doi:10.1007/978-3-642-13232-2_52

Reference : Iterated Local Search for de Novo Genomic Sequencing


	Document type :	Scientific congresses, symposiums and conference proceedings : Paper published in a journal
	Discipline(s) :	Engineering, computing & technology : Computer science
	To cite this reference:	http://hdl.handle.net/10993/16699

Title :	Iterated Local Search for de Novo Genomic Sequencing
Language :	English
Author, co-author :	Dorronsoro, Bernabé [University of Luxembourg > Interdisciplinary Centre for Security, Reliability and Trust (SNT) > >]
	Bouvry, Pascal [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC) >]
	Alba, Enrique [University of Málaga, Spain]
Publication date :	2010
Journal title :	Lecture Notes in Computer Science
Publisher :	Springer-Verlag
Volume :	6114
Pages :	428-436
Peer reviewed :	Yes
On invitation :	No
Audience :	International
ISSN :	0302-9743
e-ISSN :	1611-3349
Event name :	International Conference on Artifical Intelligence and Soft Computing
Event date :	from 13-06-2010 to 17-06-2010
Abstract :	[en] The sequencing process of a DNA chain for reading its components supposes a complex process, since only small DNA fragments can be read nowadays. Therefore, the use of optimization algorithms is required to rebuild a single chain from all the small pieces. We address here a simplified version of the problem, in which no errors in the sequencing process are allowed. The methods typically used in the literature for this problem are not satisfactory when solving realistic size instances, so there is a need for new more efficient and accurate methods. We propose a new iterated local search algorithm, highly competitive with the best algorithms in the literature, and considerably faster.
Research centres :	University of Luxembourg: High Performance Computing - ULHPC
Permalink :	http://hdl.handle.net/10993/16699
DOI :	10.1007/978-3-642-13232-2_52

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