Protein multiple sequence alignment by basic flower pollination algorithm

In this paper, a flower pollination algorithm (FPA) for the multiple sequence alignment (MSA) problem has been proposed. The FPA is a nature-inspired metaheuristic algorithm based on the pollination process of flowers flowering plants. MSA is an alignment of three or more sequences. MSA is used in many applications such as protein structure prediction, phylogenetic analysis, and genome primer identification. In research of MSA, a challenging problem is how to find the MSA that maximises the SP (Sum-of-Pairs) score. This problem is an NP-complete problem. This proposed work adapts the FPA to optimize the SP score of MSA method. The prelim results show that applying basic FPA on MSA still has room for improvement in terms of accuracy for SP score to reach global solution.