Discrete shuffled flog leaping algorithm for RNA secondary structure prediction

A discrete shuffled flog leaping algorithm is designed for the RNA secondary prediction problem. According to the characteristics of RNA folding, new search space and individual location updating rules are redefined to search the RNA secondary structure with minimal free energy in the combinatorial space of stems. The algorithm is modified by the introduction of inertia weight in particle swarm optimization algorithm (PSO) to get good balance between exploration and exploitation. The simulation results comparing with typical algorithm Mfold show that it can produce higher accuracy and faster convergence.