New Constructive Heuristics for DNA Sequencing by Hybridization

  • Christian Blum
  • Mateu Yábar Vallès
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)


Deoxyribonucleic acid (DNA) sequencing is an important task in computational biology. In recent years the specific problem of DNA sequencing by hybridization has attracted quite a lot of interest in the optimization community. However, in contrast to the development of metaheuristics, the work on simple constructive heuristics hardly received any attention. This is despite the fact that well-working constructive heuristics are often an essential component of succesful metaheuristics. It is exactly this lack of constructive heuristics that motivated the work presented in this paper. The results of our best constructive heuristic are comparable to the results of the best available metaheuristics, while using less computational resources.


Target Sequence Problem Instance Positive Error Negative Error Scatter Search 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Bains, W., Smith, G.C.: A novel method for nucleid acid sequence determination. J. of Theoretical Biology 135, 303–307 (1988)CrossRefGoogle Scholar
  2. 2.
    IuP, Y.P.L., Florentiev, V.L., Khorlin, A.A., Khrapko, K.R., Shik, V.V.: Determination of the nucleotide sequence of DNA using hybridization with oligonucleotides. a new method. Doklady Akademii Nauk SSSR 303, 1508–1511 (1988)Google Scholar
  3. 3.
    Drmanac, R., Labat, I., Brukner, R., Crkvenjakov, R.: Sequencing of megabase plus DNA by hybridization: Theory of the method. Genomics 4, 114–128 (1989)CrossRefGoogle Scholar
  4. 4.
    Pevzner, P.A.: l-tuple DNA sequencing: Computer analysis. Journal of Biomulecular Structure and Dynamics 7, 63–73 (1989)Google Scholar
  5. 5.
    Błażewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., Weglarz, J.: DNA sequencing with positive and negative errors. J. of Computational Biology 6, 113–123 (1999)CrossRefGoogle Scholar
  6. 6.
    Błażewicz, J., Formanowicz, P., Guinand, F., Kasprzak, M.: A heuristic managing errors for DNA sequencing. Bioinformatics 18(5), 652–660 (2002)CrossRefGoogle Scholar
  7. 7.
    Błażewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., Weglarz, J.: Tabu search for DNA sequencing with false negatives and false positives. European J. of Operational Research 125, 257–265 (2000)MATHCrossRefGoogle Scholar
  8. 8.
    Błażewicz, J., Glover, F., Kasprzak, M.: DNA sequencing—Tabu and scatter search combined. INFORMS J. on Computing 16(3), 232–240 (2004)CrossRefGoogle Scholar
  9. 9.
    Błażewicz, J., Glover, F., Kasprzak, M.: Evolutionary approaches to DNA sequencing with errors. Annals of Operations Research 138, 67–78 (2005)MATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    Błażewicz, J., Kasprzak, M., Kuroczycki, W.: Hybrid genetic algorithm for DNA sequencing with errors. J. of Heuristics 8, 495–502 (2002)MATHCrossRefGoogle Scholar
  11. 11.
    Endo, T.A.: Probabilistic nucleotide assembling method for sequencing by hybridization. Bioinformatics 20(14), 2181–2188 (2004)CrossRefGoogle Scholar
  12. 12.
    Bui, T.N., Youssef, W.A.: An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. In: Deb, K., et al. (eds.) GECCO 2004. LNCS, vol. 3103, pp. 908–919. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  13. 13.
    Brizuela, C.A., González, L.C., Romero, H.J.: An improved genetic algorithm for the sequencing by hybridization problem. In: Raidl, G.R., Cagnoni, S., Branke, J., Corne, D.W., Drechsler, R., Jin, Y., Johnson, C.G., Machado, P., Marchiori, E., Rothlauf, F., Smith, G.D., Squillero, G. (eds.) EvoWorkshops 2004. LNCS, vol. 3005, pp. 11–20. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  14. 14.
    Fernandes, E.R., Ribeiro, C.C.: Using an adaptive memory strategy to improve a multistart heuristic for sequencing by hybridization. In: Nikoletseas, S.E. (ed.) WEA 2005. LNCS, vol. 3503, pp. 4–15. Springer, Heidelberg (2005)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Christian Blum
    • 1
  • Mateu Yábar Vallès
    • 1
  1. 1.ALBCOM, Dept. Llenguatges i Sistemes InformàticsUniversitat Politècnica de CatalunyaBarcelonaSpain

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