Multiple Sequence Alignment Based on a Binary Particle Swarm Optimization Algorithm

Multiple sequence alignment (MSA) is a fundamental and challenging problem in the analysis of biologic sequence. The MSA problem is hard to be solved directly, for it always results in exponential complexity with the scale of the problem. In this paper, we present a novel algorithm of binary particle swarm optimization (BPSO) for MSA solving. The approach is examined by using a set of standard instances taken from the benchmark alignment database, BALIBASE. Numerical simulation results are compared with four leading multiple alignment systems and show the superiority of the proposed algorithm.