A parallel algorithm for the constrained multiple sequence alignment problem

We propose a parallel algorithm for the constrained multiple sequence alignment (CMSA) problem that seeks an optimal multiple alignment constrained to include a given pattern. We consider the dynamic programming computations in layers indexed by the symbols of the given pattern. In each layer we compute as a potential part of an optimal alignment for the CMSA problem, shortest paths for multiple sources and multiple destinations. These shortest paths problems are independent from one another (which enables parallel execution), and each can be solved using an A* algorithm specialized for the shortest paths problem for multiple sources and multiple destinations. The final step of our algorithm solves a single source single destination shortest path problem. Our experiments on real sequences show that our algorithm is faster in general than the existing sequential dynamic programming solutions.