International Conference on Electronics, Information and Communication Engineering (EICE 2012)
135 A Heuristic Algorithm of RNA Pseudoknotted Structure Prediction Based on Stem
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Minimum free energy method is adopted widely to predict RNA secondary structure. Based on the relative stability of the stems in RNA molecules, a heuristic algorithm is presented to predict RNA pseudo-knotted structure, the algorithm takes O(n3) time and O(n2) space, this algorithm not only reduces the time complexity to O(n3), but also widens the maximum length of the sequence. The preliminary experimental test on the RNA subsequences in PseudoBase confirm that the algorithm outperforms other known algorithms in predicting accuracy, time complexity and space complexity.