A* Algorithms for the Constrained Multiple Sequence Alignment Problem

It is well known that A algorithm reduces the search space in many applications. For shortest path computations, the algorithm uses a heuristic estimator which can better guide the search to the destination. It allocates memory dynamically to store only the necessary vertices, which are those vertices in its open list and close list. Therefore, an A algorithm for the shortest paths search problem is much more space efficient than ordinary search algorithm such as the dynamic programming algorithm and the Dijkstra algorithm. The constrained multiple sequence alignment problem (CMSA) aims to align similar subsequences in the same region under the guidance of a given pattern (constraint). The CMSA problem can be considered as an optimal path search problem in the dynamic programming matrix. In this paper, we propose two A-based algorithms which we experimentally show that in practice they solve the CMSA problem using much less memory than does the ordinary dynamic programming algorithm.