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)

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.

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References

  1. 1.
    Setubal, J., Meidanis, J.: Introduction to Computational Molecular Biology, chapter 4 - Fragment Assembly of DNA, pp. 105–139. University of Campinas, Brazil (1997)Google Scholar
  2. 2.
  3. 3.
    Sutton, G.G., White, O., Adams, M.D., Kerlavage, A.R.: TIGR Assembler: A new tool for assembling large shotgun sequencing projects. In: Genome Science & Technology, pp. 9–19 (1995)Google Scholar
  4. 4.
    Chen, T., Skiena, S.S.: Trie-based data structures for sequence assembly. In: The Eighth Symposium on Combinatorial Pattern Matching, pp. 206–223 (1998)Google Scholar
  5. 5.
    Huang, X., Madan, A.: CAP3: A DNA sequence assembly program. Genome Research 9, 868–877 (1999)CrossRefGoogle Scholar
  6. 6.
    Myers, E.W.: Towards simplifying and accurately formulating fragment assembly. Journal of Computational Biology 2(2), 275–290 (2000)Google Scholar
  7. 7.
    Pevzner, P.A.: Computational molecular biology: An algorithmic approach. MIT Press, London (2000)MATHGoogle Scholar
  8. 8.
    Luque, G., Alba, E.: Metaheuristics for the DNA Fragment Assembly Problem. International Journal of Computational Intelligence Research 1(2), 98–108 (January 2006)Google Scholar
  9. 9.
    Parsons, R., Forrest, S., Burks, C.: Genetic algorithms, operators, and DNA fragment assembly. Machine Learning 21, 11–33 (1995)Google Scholar
  10. 10.
    Li, L., Khuri, S.: A comparison of DNA fragment assembly algorithms. In: International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, pp. 329–335 (2004)Google Scholar
  11. 11.
    Lin, S., Kernighan, B.W.: An effective heuristic algorithm for TSP. Operations Research 21, 498–516 (1973)MATHMathSciNetCrossRefGoogle Scholar
  12. 12.
    Engle, M.L., Burks, C.: Artificially generated data sets for testing DNA fragment assembly algorithms. Genomics 16 (1993)Google Scholar
  13. 13.
    Jing, Y., Khuri, S.: Exact and heuristic algorithms for the DNA fragment assembly problem. In: Proceedings of the IEEE Computer Society Bioinformatics Conference, pp. 581–582. IEEE Press, New York (2003)Google Scholar

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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