A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
Identifieur interne : 004D28 ( Main/Exploration ); précédent : 004D27; suivant : 004D29A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
Auteurs : Ernst Althaus [Allemagne] ; Stefan Canzar [France]Source :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
Abstract: 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.
Url:
DOI: 10.1007/978-3-540-73556-4_29
Affiliations:
- Allemagne, France
- Grand Est, Lorraine (région), Sarre (Land)
- Sarrebruck, Vandœvre-lès-Nancy
- Université Henri Poincaré
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