An Approximation Scheme for RNA Folding Structure Prediction Including Pseudoknots

Abstract

The paper further investigates the computational problem and complexity of predicting Ribonucleic Acid structure. In order to find a way to optimize the Ribonucleic Acid pseudoknotted structure, we investigate the Ribonucleic Acid pseudoknotted structure based on thermal dynamic model, computational methods, minimum free energy are adopted to predict Ribonucleic Acid structure. The contribution of this paper is to obtain an efficient Approximation algorithm for finding RNA pseudoknotted structure, compared with other algorithms, the algorithm takes O(n3) time and O(n2) space. The experimental test in PseudoBase shows that the algorithm is more effective and exact than other algorithms, and the algorithm can predict arbitrary pseudoknots. And we also give a proof of existing 1+e (e>0) Polynomial Time Approximation Scheme(PTAS) in Searching Maximum Number of Stackings.