New Heuristic Algorithm of RNA Secondary Structure Prediction with Pseudoknots

Based on the relative stability of the n-stems in RNA molecules, Minimum free energy method is adopted widely to predict RNA secondary structure, a heuristic algorithm is presented to predict RNA pseudoknotted structure, the algorithm takes O(n
³
) time and O(n
²
) space. This algorithm not only reduces the time complexity to O(n
³
), but also widens the maximum length of the sequence. The preliminary experimental test on the RNA sub-sequences in PseudoBase confirm that the algorithm outperforms other known algorithms in predicting accuracy, sensitivity and specificity.