¹ School of Computer Science and Technology, Shandong University, Jinan, China
² School of Computer Science and Technology, Shandong Jianzhu University, Jinan, China

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Abstract—Computational models and methods for predicting secondary structure of RNA sequence are in demand. Based on MFE principle and the relative stability of the n-stems in RNA molecules, Minimum Free Energy method is adopted widely to predict RNA secondary structure. An improved heuristic algorithm is presented to predict RNA pseudoknotted structure, and it can compute arbitrary pseudoknots. The algorithm requires 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 RNA sequence. The preliminary experimental test on the RNA families in PseudoBase shows that the algorithm is more effective than the existing algorithms.

Index Terms—RNA secondary structure, pseudoknots, nstem, heuristic algorithm

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Cite: Zhendong Liu and Daming Zhu, " New Heuristic Algorithm of RNA Structure Prediction including Pseudoknots," Journal of Computers vol. 8, no. 2, pp. 279-283, 2013.