A hybrid solver for protein multiple sequence alignment problem

In this work, a novel hybrid model called PSOSA for solving multiple sequence alignment (MSA) problem is proposed. The developed approach is a combination between particle swarm optimization (PSO) algorithm and simulated annealing (SA) technique. In our PSOSA approach, PSO is exploited in global search, but it is easily trapped into local optimum and may lead to premature convergence. SA is incorporated as local improvement approach to overcome local optimum problem and intensify the search in local regions to improve solution quality. Numerical results on BAliBASE benchmark have shown the effectiveness of the proposed method and its ability to achieve good quality solutions when compared with those given by other existing methods.