A new local search algorithm for the DNA fragment assembly problem

Authors:
Enrique Alba;Gabriel Luque
Affiliations:
Grupo GISUM, Departamento de LCC, E.T.S.I. Informática, Málaga, Spain;Grupo GISUM, Departamento de LCC, E.T.S.I. Informática, Málaga, Spain
Venue:
EvoCOP'07 Proceedings of the 7th European conference on Evolutionary computation in combinatorial optimization
Year:
2007

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Abstract

In this paper we propose and study the behavior of a new heuristic algorithm for the DNA fragment assembly problem: PALS. The DNA fragment assembly is a problem to be solved in the early phases of the genome project and thus is very important since the other steps depend on its accuracy. This is an NP-hard combinatorial optimization problem which is growing in importance and complexity as more research centers become involved on sequencing new genomes. Various heuristics, including genetic algorithms, have been designed for solving the fragment assembly problem, but since this problem is a crucial part of any sequencing project, better assemblers are needed. Our proposal is a very efficient assembler that allows to find optimal solutions for large instances of this problem, considerably faster than its competitors and with high accuracy.