Particle Swarm Optimization with Probability Statistic for Biological Multiple Sequence Alignment

Multiple sequence alignment is a researched hotspot in Bioinformatics.With the problem of low precision of large-scale multiple sequence alignment,a new multiple sequence alignment algorithm based on particle swarm optimization with probability statistic and automatic adaptive mutation(MSA_PMPSO) was proposed.MSA_PMPSO generates new solutions with the help of a model which is established according to the distributional probability of high quality solutions.This design may enhance the study capability of particles and improve the accuracy of alignment.Also the algorithm introduces the fitness variance,the expected optimal solution and the mutation operation,which makes for jumping out of the local optimum.The experimental results of 142 benchmarks from the BALIBASE prove that the proposed algorithm is feasible and valid.Especially,it is more advantageous than existing algorithms when the large-scale closed genetic long sequences are aligned.