HSRNAFold: A harmony search algorithm for RNA secondary structure prediction based on minimum free energy

Current physical methods for RNA structure determination are time consuming and expensive; thus the methods for the computational prediction of structure are necessary. Various algorithms have been used for RNA structure prediction including dynamic programming and meta-heuristic algorithms. This paper proposes a meta-heuristic harmony search algorithm (HSRNAFold) for finding RNA secondary structure with minimum free energy and similarity to the native structure. HSRNAFold is compared to dynamic programming techniques: RNAFold and the benchmark Mfold. The results show that HSRNAFold is comparable to dynamic programming to find the minimum free energies for all RNA test sequences. The proposed method is efficient and promising to predict RNA secondary structure based on minimum free energy.