A novel method for RNA secondary structure prediction

In this paper, we propose PSOfold, a particle swarm optimization for RNA secondary structure prediction. PSOfold is based on the recently published IPSO. We present two strategies to improve the performance of IPSO. Firstly, in order to boost the competence in searching an optimal solution, fuzzy logic control is used to adaptively adjust the parameters in PSO. Accordingly, three fuzzy logic controls are designed by which the inertia weight, learning factors and the number of ants are tuned respectively. Secondly, to further settle the stem permutation problem, we put forward a solution conversion strategy (SCS), which can transform discrete values of stems into an ordered stem combination, thereby supplying an enhanced solution to evaluation of objective function. An evaluation of the performance of PSOfold in terms of prediction accuracy is made via comparison with one dynamic programming algorithm mfold and four metaheuristics, IPSO, ACRNA, RnaPredict, SARNA-Predict and mfold for ten individual known structures. PSOfold is able to predict structures with higher prediction accuracy than the other metaheuristic based methods on certain sequences, and has comparable performance compared with mfold.