Multiple sequence alignment by ant colony optimization and divide-and-conquer

Abstract

Multiple sequence alignment is a common task in molecular biology and bioinformatics. Obtaining an accurate alignment of protein sequences is a difficult computational problem because many heuristic techniques cannot achieve optimality in a reasonable running time. A novel multiple sequence alignment algorithm based on ant colony optimization and divide-and-conquer technique is proposed. The algorithm divides a set of sequences into several subsections vertically by bisecting the sequences recursively using the ant colony optimization method. We also present two methods that adaptively adjust the parameters and update the pheromones to avoid local optimal traps. Experimental results show that the algorithm can achieve high quality solution and significantly reduce the running time. © Springer-Verlag Berlin Heidelberg 2006.