Abstract
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.
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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)
Bockenhauer, H.J., Bongartz, D.: Algorithmic Aspects of Bioinformatics. Springer (2007)
DeRonne, K.W., Karypis, G.: Pareto optimal pairwise sequence alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(2), 481–493 (2013)
Erhgott, M.: Multicriteria optimization. Springer (2005)
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)
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)
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)
Paquete, L., Schiavinotto, T., Stützle, T.: On local optima in multiobjective combinatorial optimization problems. Annals of Operations Research 156(1), 83–97 (2007)
Paquete, L., Matias, P., Abbasi, M., Pinheiro, M.: MOSAL: Software tools for multiobjective sequence alignment. Source Code for Biology and Medicine, 9(2) (2014)
Roytberg, M.A., Semionenkov, M.N., Tabolina, O.I.: Pareto-optimal alignment of biological sequences. Biophysics 44(4), 565–577 (1999)
Schnattinger, T., Schöning, U., Kestler, H.: Structural RNA alignment by multi-objective optimization. Bioinformatics 29(13), 1607–1613 (2013)
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)
Taneda, A.: Multi-objective pairwise RNA sequence alignment. Bioinformatics 26(19), 2383–2390 (2010)
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)
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)
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)
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Abbasi, M., Paquete, L., Pereira, F.B. (2015). Local Search for Multiobjective Multiple Sequence Alignment. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9044. Springer, Cham. https://doi.org/10.1007/978-3-319-16480-9_18
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DOI: https://doi.org/10.1007/978-3-319-16480-9_18
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