The Algorithm and Scheme of Prediction in RNA Folding Structure with Pseudoknots

Abstract

The prediction of RNA structure with pseudoknots is an NP-hard problem. According to minimum free energy models and computational methods, we investigate the RNA pseudoknotted structure. The paper presents an efficient algorithm for predicting RNA structure with pseudoknots, and the algorithm takes O(n3) time and O(n2) space. The experimental tests in Rfam10.1 and PseudoBase indicate that the algorithm is more effective and precise, and the algorithm can predict arbitrary pseudoknots. We also present several types of pseudoknots considered in RNA folding structure, and analysis possible transitions between types of pseudoknots.