The Application of an Improved Particle Swarm Optimization (PSO) Algorithm in Pairwise Sequence Alignment

Abstract

In this paper, we applied an existing particle swarm optimization algorithm to biological pairwise sequence alignment problem. In addition, we improved the basic algorithm according to sequence characteristics. This improved algorithm provides constraint conditions of the initial position of particles and the mobile strategy in motion, taking account of the other particle swarm's next generation optimal value into the current ones. And the experiments shows that the improved algorithm have being reduced the possibility of being trapped into their own local optimization, enhanced the ability of scanning and improved the performance of the basic algorithm efficiently.