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)

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.

Keywords

Multiple sequence alignment Local search Multiobjective optimization 

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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

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