An effective cooperative aligner to resolve multiple-sequence alignment problem

Abstract

In this research work, we propose a new cooperative aligner based on metaheuristics to find an approximate solution to the multiple-sequence alignment (MSA) problem. The developed approach named HPSOSA apply in the first stage the particle swarm optimisation (PSO) with a crossover operator as a move mechanism for each particle. In the second stage, simulated annealing is incorporated in order to improve worst solutions in the population and to help HPSOSA to escape from local optimum alignment. Simulation results on BaliBASE benchmarks have demonstrated the capability of the proposed method to obtain better results for the MSA problem compared to those produced by some literature works in the same field.