Local Search for Multiobjective Multiple Sequence Alignment

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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