Journal of Heuristics

, Volume 13, Issue 3, pp 209–225 | Cite as

Sequencing by hybridization: an enhanced crossover operator for a hybrid genetic algorithm

  • Carlos A. Brizuela
  • Luis C. González-Gurrola
  • Andrei Tchernykh
  • Denis Trystram


This paper presents a genetic algorithm for an important computational biology problem. The problem appears in the computational part of a new proposal for DNA sequencing denominated sequencing by hybridization. The general usage of this method for real sequencing purposes depends mainly on the development of good algorithmic procedures for solving its computational phase. The proposed genetic algorithm is a modified version of a previously proposed hybrid genetic algorithm for the same problem. It is compared with two well suited meta-heuristic approaches reported in the literature: the hybrid genetic algorithm, which is the origin of our proposed variant, and a tabu-scatter search algorithm. Experimental results carried out on real DNA data show the advantages of using the proposed algorithm. Furthermore, statistical tests confirm the superiority of the proposed variant over the state-of-the-art heuristics.


Sequencing by hybridization Hybrid genetic algorithm Greedy crossover 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bains, W., Smith, G.: A novel method for nucleic acid sequence determination. J. Theor. Biol. 135, 303–307 (1988) CrossRefGoogle Scholar
  2. Blazewicz, J., Kasprzak, M.: Complexity of DNA sequencing by hybridization. J. Theor. Comput. Sci. 290, 1459–1473 (2003) zbMATHCrossRefMathSciNetGoogle Scholar
  3. Blazewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W., Weglarz, J.: DNA sequencing with positive and negative errors. J. Comput. Biol. 6, 113–123 (1999) Google Scholar
  4. Blazewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W., Weglarz, J.: Tabu search for DNA sequencing with false negatives and false positives. Eur. J. Oper. Res. 125, 257–265 (2000) zbMATHCrossRefMathSciNetGoogle Scholar
  5. Blazewicz, J., Formanowicz, P., Guinand, F., Kasprzak, M.: A heuristic managing errors for DNA sequencing. J. Bioinformatics 18(5), 652–660 (2002a) CrossRefGoogle Scholar
  6. Blazewicz, J., Kasprzak, M., Kuroczycki, W.: Hybrid genetic algorithm for DNA sequencing with errors. J. Heuristics 8, 495–502 (2002b) zbMATHCrossRefGoogle Scholar
  7. Blazewicz, J., Glover, F., Kasprzak, M.: DNA sequencing-tabu and scatter search combined. INFORMS J. Comput. 16(3), 232–240 (2004) CrossRefMathSciNetGoogle Scholar
  8. Brizuela, C.A., González, L., Romero, H.J.: An improved genetic algorithm for the sequencing by hybridization problem. In: Raidl, G. et al. (eds.) Applications of Evolutionary Computing. Lecture Notes in Computer Science, vol. 3005, pp. 11–20. Springer, Berlin (2004) Google Scholar
  9. Bui, T.N., Youseef, W.A.: An enhanced genetic algorithm for DNA sequencing by hybridization with positive and negative errors. In: Deb, K. (ed.) Proceedings of the Genetic and Evolutionary Computation Conference, Seattle, Washington, United States. Lecture Notes in Computer Science, vol. 3103, pp. 908–919. Springer, Berlin (2004) Google Scholar
  10. Caviani, P., Solas, D., Sullivan, E., Cronin, M., Holmes, C., Fodor, S.: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Nat. Acad. Sci. USA 91, 5022–5026 (1994) CrossRefGoogle Scholar
  11. Garey, M., Johnson, D.: Computers and Intractability: A Guide to the Theory of NP-Completeness, 21st edn. Freeman, New York (1978) Google Scholar
  12. Goldberg, D.: Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, Reading (1989) zbMATHGoogle Scholar
  13. Grefenstette, J., Gopal, R., Rosmaita, B., Gucht, D.V.: Genetic algorithms for the travelling salesman problem. In: Grenfestette, J.J. (ed.) Proceedings of the First International Conference on Genetic Algorithms and their Applications, vol. 1, pp. 160–168. Erlbaum, Hillsdale (1988) Google Scholar
  14. Hirschhom, J., Sklar, P., Lindblad-Toh, K., Lim, Y.-M., RuizGutierrez, M., Bolk, S., Langhorst, B., Schaffner, S., Wichester, E., Lander, E.: SBE-TAGS: An arraybased method for efficient single-nucleotide polymorphism genotyping. Proc. Nat. Acad. Sci. USA 97, 12164–12169 (2000) CrossRefGoogle Scholar
  15. Holland, J.: Adaptation in Natural and Artificial Systems. University of Michigan Press, Ann Harbor (1975) Google Scholar
  16. Iduri, R.M., Waterman, M.S.: A new algorithm for DNA sequence assembly. J. Comput. Biol. 2(2), 291–306 (1995) CrossRefGoogle Scholar
  17. Krebs, J., Dunaway, M.: DNA length is a critical parameter for eukaryotic transcription in vivo. Mol. Cell. Biol. 16(10), 5821–5829 (1996) Google Scholar
  18. Maxam, A., Gilbert, W.: A new method for sequencing DNA. Proc. Nat. Acad. Sci. 74, 560–564 (1977) CrossRefGoogle Scholar
  19. Pevzner, P.: l-tuple DNA sequencing: computer analysis. J. Biomol. Struct. Dyn. 7, 63–73 (1989) Google Scholar
  20. Sanger, F., Coulson, A.: The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 87, 107–110 (1978) CrossRefGoogle Scholar
  21. Southern, E.: United Kingdom patent application GB8810400 (1988) Google Scholar
  22. Southern, E., Maskos, U., Elder, J.K.: Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13, 1008–1017 (1992) CrossRefGoogle Scholar
  23. Stoye, J.: Multiple sequence alignment with the divide-and-conquer method. Gene 211(2), GC45–GC56 (1998) CrossRefGoogle Scholar
  24. Zar, J.H.: Biostatistical Analysis, 4th edn. Prentice-Hall, Englewood Cliffs (1999) Google Scholar
  25. Zhang, J., Wu, L., Zhang, X.: Reconstruction of DNA sequencing by hybridization. J. Bioinform. 19(1), 14–21 (2003) CrossRefzbMATHGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Carlos A. Brizuela
    • 1
  • Luis C. González-Gurrola
    • 2
  • Andrei Tchernykh
    • 1
  • Denis Trystram
    • 3
  1. 1.Computer Sciences DepartmentCICESE Research CenterEnsenadaMexico
  2. 2.Instituto Tecnológico Superior de Santiago PapasquiaroSantiago PapasquiaroMexico
  3. 3.ID-Institut IMAGGrenoble Cedex 9France

Personalised recommendations