A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4616)


We present a branch-and-bound (bb) algorithm for the multiple sequence alignment problem (MSA), one of the most important problems in computational biology. The upper bound at each bb node is based on a Lagrangian relaxation of an integer linear programming formulation for MSA. Dualizing certain inequalities, the Lagrangian subproblem becomes a pairwise alignment problem, which can be solved efficiently by a dynamic programming approach. Due to a reformulation w.r.t. additionally introduced variables prior to relaxation we improve the convergence rate dramatically while at the same time being able to solve the Lagrangian problem efficiently. Our experiments show that our implementation, although preliminary, outperforms all exact algorithms for the multiple sequence alignment problem.


Multiple Sequence Alignment Integer Linear Programming Target Node Lagrangian Relaxation Pairwise Alignment 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  1. 1.Max-Planck Institut für Informatik, Stuhlsatzenhausweg 85, D-66123 SaarbrückenGermany
  2. 2.Université Henri Poincaré, LORIA, B.P. 239, 54506 Vandœvre-lès-NancyFrance

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