MEMSA: A Robust Parisian EA for Multidimensional Multiple Sequence Alignment

  • Julie D. Thompson
  • Renaud Vanhoutrève
  • Pierre Collet
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10764)


This paper describes a new approach for the multiple alignment of biological sequences (DNA or proteins) using a Parisian Evolution approach called MEMSA, for Multidimensional Evolutionary Multiple Sequence Alignment, coded using the EASEA platform. This approach evolves individual sub-alignments called “patches” that are used to create a new kind of Multiple Sequence Alignment where alternative solutions are computed simultaneously using different fitness functions. Solutions are generated by combining coherent sets of high-scoring individuals that are used to reconstruct multi-dimensional multiple sequence alignments. The alignments of this prototype version show a quality comparable to ClustalW (one of the most widely used existing methods) on the 218 samples of the BAliBASE benchmark in reasonable time.



We would like to thank the members of the BISTRO Bioinformatics Platform in Strasbourg for their support. This work was supported by the Agence Nationale de la Recherche (BIPBIP: ANR-10-BINF-03-02), the Région Alsace and Institute funds from the CNRS, the Université de Strasbourg and the Faculté de Médecine de Strasbourg.


  1. 1.
    Blackburne, B.P., Whelan, S.: Measuring the distance between multiple sequence alignments. Bioinformatics 28(4), 495–502 (2012)CrossRefGoogle Scholar
  2. 2.
    Collet, P., Lutton, E., Raynal, F., Schoenauer, M.: Polar IFS+Parisian genetic programming=efficient IFS inverse problem solving. Genetic Program. Evolvable Mach. 1(4), 339–361 (2000). CrossRefzbMATHGoogle Scholar
  3. 3.
    Collet, P., Lutton, E., Schoenauer, M., Louchet, J.: Take it EASEA. In: Schoenauer, M., Deb, K., Rudolph, G., Yao, X., Lutton, E., Merelo, J.J., Schwefel, H.-P. (eds.) PPSN 2000. LNCS, vol. 1917, pp. 891–901. Springer, Heidelberg (2000). CrossRefGoogle Scholar
  4. 4.
    Do, C.B., Mahabhashyam, M.S., Brudno, M., Batzoglou, S.: Probcons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15(2), 330–340 (2005)CrossRefGoogle Scholar
  5. 5.
    Edgar, R.C.: Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5), 1792–1797 (2004)CrossRefGoogle Scholar
  6. 6.
    Zhu, H., He, Z., Jia, Y.: A novel approach to multiple sequence alignment using multiobjective evolutionary algorithm based on decomposition. IEEE J. Biomed. Health Inform. 20, 717–727 (2016)CrossRefGoogle Scholar
  7. 7.
    Hayes-Roth, F.: Review of “adaptation in natural and artificial systems by John H. Holland”. The University of Michigan Press (1975). SIGART Bull. 53, 15 (1975).
  8. 8.
    Henikoff, S., Henikoff, J.G.: Amino acid substitution matrices from protein blocks. Proc. Nat. Acad. Sci. 89(22), 10915–10919 (1992). CrossRefGoogle Scholar
  9. 9.
    Holland, J.H.: Escaping brittleness: the possibilities of general-purpose learning algorithms applied to parallel rule-based systems. In: Computation & Intelligence, pp. 275–304. American Association for Artificial Intelligence, Menlo Park (1995).
  10. 10.
    Katoh, K., Standley, D.M.: MAFFT: iterative refinement and additional methods. In: Multiple Sequence Alignment Methods, pp. 131–146. Humana Press, Totowa (2014)Google Scholar
  11. 11.
    Kaya, M., Sarhan, A., Alhajj, R.: Multiple sequence alignment with affine gap by using multi-objective genetic algorithm. Comput. Methods Prog. Biomed. 114, 38–49 (2014)CrossRefGoogle Scholar
  12. 12.
    Cai, L., Juedes, D., Liaknovitch, E.: Evolutionary computation techniques for multiple sequence alignment. In: Proceedings of the IEEE Congress on Evolutionary Computation (2000)Google Scholar
  13. 13.
    Larkin, M., Blackshields, G., Brown, N., Chenna, R., McGettigan, P., McWilliam, H., Valentin, F., Wallace, I., Wilm, A., Lopez, R., Thompson, J., Gibson, T., Higgins, D.: Clustal w and clustal x version 2.0. Bioinformatics 23, 2947–2948 (2007)CrossRefGoogle Scholar
  14. 14.
    Lassmann, T., Sonnhammer, E.L.: Kalign - an accurate and fast multiple sequence alignment algorithm. BMC Bioinf. 6(1), 298 (2005)CrossRefGoogle Scholar
  15. 15.
    Maitre, O., Krüger, F., Querry, S., Lachiche, N., Collet, P.: EASEA: specification and execution of evolutionary algorithms on GPGPU. Soft Comput. 16(2), 261–279 (2011)CrossRefGoogle Scholar
  16. 16.
    Nguyen, H.D., Yoshihara, I., Yamamori, K., Yasunaga, M.: Aligning multiple protein sequences by parallel hybrid genetic algorithm. Genome Inform. 13, 123–132 (2002)Google Scholar
  17. 17.
    Notredame, C., Higgins, D.G.: Saga: sequence alignment by genetic algorithm. Nucleic Acids Res. 24(8), 1515–1524 (1996)CrossRefGoogle Scholar
  18. 18.
    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). Structure, Function and BioInformaticsCrossRefGoogle Scholar
  19. 19.
    Thompson, J.D., Linard, B., Lecompte, O., Poch, O.: A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One 6(3), e18093 (2011)CrossRefGoogle Scholar
  20. 20.
    Thompson, J.D., Plewniak, F., Ripp, R., Thierry, J.C., Poch, O.: Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol. 314(4), 937–951 (2001). CrossRefGoogle Scholar
  21. 21.
    Wilson, S.W., Goldberg, D.E.: A critical review of classifier systems. In: Proceedings of the 3rd International Conference on Genetic Algorithms, pp. 244–255. Morgan Kaufmann Publishers Inc., San Francisco (1989).
  22. 22.
    Zhang, C., Wong, A.: A genetic algorithm for multiple molecular sequence alignment. Comput. Appl. Biosci. 13, 565–581 (1997)Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.ICube laboratory, UMR CNRS 7357, Strasbourg UniversityStrasbourgFrance
  2. 2.Fédération de Médecine Translationnelle de Strasbourg, CS-DC UNESCO UniTwinStrasbourgFrance

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