A New Local Search Algorithm for the DNA Fragment Assembly Problem

  • Enrique Alba
  • Gabriel Luque
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4446)


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.


Execution Time Large Instance Shotgun Sequencing Pattern Match Algorithm Single Contig 
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Copyright information

© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Enrique Alba
    • 1
  • Gabriel Luque
    • 1
  1. 1.Grupo GISUM, Departamento de LCC, E.T.S.I. Informática, Campus Teatinos, 29071 Málaga (Spain) 

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