Approximation algorithm of the RNA pseudoknotted structure prediction baesed on MFE

Determination of Ribonucleic Acid structure is challenging, in order to optimize the RNA pseudoknotted structure,the paper investigates the computational problem and complexity of predicting RNA structure. A new computational method and model with minimum free energy are adopted to predict RNA structure. The main contribution of the paper is to achieves an efficient approximation algorithm for finding RNA pseudoknotted structure and nested structures. We have compared with other algorithms in time complexity and space complexity, the approximation algorithm takes O(n³) time and O(n²) space,where n is the length of the RNA sequences. The experimental tests for a large database of RNA show that the algorithm is more exact and effective than the algorithms, the algorithm can predict arbitrary pseudoknots, and improve the a predicting accuracy.