Multiple sequence alignment using modified dynamic programming and particle swarm optimization

Abstract

Dynamic Programming (DP) is widely used in Multiple Sequence Alignment (MSA) problems. However, when the number of the considered sequences is more than two, multiple dimensional DP may suffer from large storage and computational complexities. Often, progressive pairwise DP is employed for MSA. However, such an approach also suffers from local optimum problems. In this paper, we present a hybrid algorithm for MSA. The algorithm combines the pairwise DP and the particle swarm optimization (PSO) techniques to overcome the above drawbacks. In the algorithm, pairwise DP is used to align sequences progressively and PSO is employed to avoid the result of alignment being trapped into local optima. Several existing MSA tools are employed for comparison. The experimental results show excellent performance of the proposed algorithm.