DCA based algorithms for multiple sequence alignment (MSA)

In the last years many techniques in bioinformatics have been developed for the central and complex problem of optimally aligning biological sequences. In this paper we propose a new optimization approach based on DC (Difference of Convex functions) programming and DC Algorithm (DCA) for the multiple sequence alignment in its equivalent binary linear program, called “Maximum Weight Trace” problem. This problem is beforehand recast as a polyhedral DC program with the help of exact penalty techniques in DC programming. Our customized DCA, requiring solution of a few linear programs, is original because it converges after finitely many iterations to a binary solution while it works in a continuous domain. To scale-up large-scale (MSA), a constraint generation technique is introduced in DCA. Preliminary computational experiments on benchmark data show the efficiency of the proposed algorithm DCAMSA, which generally outperforms some standard algorithms.