Predicting algorithm for RNA pseudoknotted structure

Abstract

Pseudoknots are a frequent RNA structure. Based on the relative stability of the stems in RNA molecules, an algorithm is presented to predict RNA pseudoknotted structure,the introduced algorithm takes O(n3) time and O(n) space and outperforms other known algorithms in predicting accuracy. This algorithm not only reduces the time complexity to O(n3), but also widens the maximum length of the sequence The experimental results on the RNA sub-sequences in PseudoBase indicate that the algorithm has good accuracy, sensitivity and specificity.