Prediction of RNA Secondary Structure Using Quantum-inspired Genetic Algorithms

Background: The prediction of RNA secondary structure using optimization algorithms is key to understand the real structure of an RNA. Evolutionary algorithms (EAs) are popular strategies for RNA secondary structure prediction. However, compared to most state-of-the-art software based on DPAs, the performances of EAs are a bit far from satisfactory. Objective: Therefore, a more powerful strategy is required to improve the performances of EAs when applied to the prediciton of RNA secondary structures. Methods: The idea of quantum computing is introduced here yielding a new strategy to find all possible legal paired-bases with the constraint of minimum free energy. The sate of a stem pool with size N is encoded as a population of QGA, which is represented by N quantum bits but not classical bits. The updating of populations is accomplished by so-called quantum crossover operations, quantum mutation operations and quantum rotation operations. Results: The numerical results show that the performances of traditional EAs are significantly improved by using QGA with regard to not only prediction accuracy and sensitivity but also complexity. Moreover, for RNA sequences with middle-short length, QGA even improves the state-of-art software based on DPAs in terms of both prediction accuracy and sensitivity. Conclusion: This work sheds an interesting light on the applications of quantum computing on RNA structure prediction.