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COCOA
2007
Springer

A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem

13 years 8 months ago
A Lagrangian Relaxation Approach for the Multiple Sequence Alignment Problem
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.
Ernst Althaus, Stefan Canzar
Added 07 Jun 2010
Updated 07 Jun 2010
Type Conference
Year 2007
Where COCOA
Authors Ernst Althaus, Stefan Canzar
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