Local Search for Multiobjective Multiple Sequence Alignment

  • Maryam Abbasi
  • Luís Paquete
  • Francisco B. Pereira
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9044)


Recently, there has been a growing interest on the multiobjective formulation of optimization problems that arise in bioinformatics, such as sequence alignment. In this work, we consider the multiobjective multiple sequence alignment, with the goal of maximizing the substitution score and minimizing the number of indels. We introduce several local search approaches for this problem. Several neighborhood definitions and perturbations are presented and discussed. The local search algorithms are tested experimentally on a wide range of instances.


Multiple sequence alignment Local search Multiobjective optimization 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Abbasi, M., Paquete, L., Liefooghe, A., Pinheiro, M., Matias, P.: Improvements on bicriteria pairwise sequence alignment: Algorithms and applications. Bioinformatics 29(8), 996–1003 (2013)CrossRefGoogle Scholar
  2. 2.
    Bockenhauer, H.J., Bongartz, D.: Algorithmic Aspects of Bioinformatics. Springer (2007)Google Scholar
  3. 3.
    DeRonne, K.W., Karypis, G.: Pareto optimal pairwise sequence alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(2), 481–493 (2013)CrossRefGoogle Scholar
  4. 4.
    Erhgott, M.: Multicriteria optimization. Springer (2005)Google Scholar
  5. 5.
    Handl, J., Kell, D.B., Knowles, J.D.: Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics 4(2), 279–292 (2007)CrossRefGoogle Scholar
  6. 6.
    Lourenço, H.R., Martin, O., Stützle, T.: Iterated local search. In: Handbook of Metaheuristics. International Series in Operations Research & Management Science, vol. 57, p. 321. Kluwer Academic Publishers (2013)Google Scholar
  7. 7.
    Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48, 443–453 (1970)CrossRefGoogle Scholar
  8. 8.
    Paquete, L., Schiavinotto, T., Stützle, T.: On local optima in multiobjective combinatorial optimization problems. Annals of Operations Research 156(1), 83–97 (2007)CrossRefMATHMathSciNetGoogle Scholar
  9. 9.
    Paquete, L., Matias, P., Abbasi, M., Pinheiro, M.: MOSAL: Software tools for multiobjective sequence alignment. Source Code for Biology and Medicine, 9(2) (2014)Google Scholar
  10. 10.
    Roytberg, M.A., Semionenkov, M.N., Tabolina, O.I.: Pareto-optimal alignment of biological sequences. Biophysics 44(4), 565–577 (1999)Google Scholar
  11. 11.
    Schnattinger, T., Schöning, U., Kestler, H.: Structural RNA alignment by multi-objective optimization. Bioinformatics 29(13), 1607–1613 (2013)CrossRefGoogle Scholar
  12. 12.
    Sievers, F., Wilm, A., Dineen, D.G., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J.D., Higgins, D.G.: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7, 539 (2011)CrossRefGoogle Scholar
  13. 13.
    Taneda, A.: Multi-objective pairwise RNA sequence alignment. Bioinformatics 26(19), 2383–2390 (2010)CrossRefGoogle Scholar
  14. 14.
    Thompson, J.D., Koehl, P., Ripp, R., Poch, O.: BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins 61(1), 127–136 (2005)CrossRefGoogle Scholar
  15. 15.
    Zitzler, E., Thiele, L.: Multiobjective optimization using evolutionary algorithms - A comparative case study. In: Eiben, A.E., Bäck, T., Schoenauer, M., Schwefel, H.-P. (eds.) PPSN 1998. LNCS, vol. 1498, pp. 292–301. Springer, Heidelberg (1998)CrossRefGoogle Scholar
  16. 16.
    Zitzler, E., Thiele, L., Laumanns, M., Fonseca, C.M., Grunert da Fonseca, V.: Performance assessment of multiobjective optimizers: An analysis and review. IEEE Transactions on Evolutionary Computation 7(2), 117–132 (2003)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Maryam Abbasi
    • 1
  • Luís Paquete
    • 1
  • Francisco B. Pereira
    • 1
    • 2
  1. 1.CISUC, Department of Informatics EngineeringUniversity of CoimbraPortugal
  2. 2.Polytechnic Institute of CoimbraPortugal

Personalised recommendations