Multiple Sequence Alignment Based on Chaotic PSO

This paper introduces a new improved algorithm called chaotic PSO (CPSO) based on the thought of chaos optimization to solve multiple sequenced; alignment. For one thing, the chaotic variables are generated between 0 and when initializing the population so that the particles are distributed uniformly in the solution space. For another thing, the chaotic sequences are generated using the Logistic mapping function in order to make chaotic search and strengthen the diversity of the population. The simulation results of several benchmark data sets of BAliBase show that the improved algorithm is effective and has good performances for the data sets with different similarity.