Abstract
It is NP-hard problem of predicting RNA structure with pseudoknots. According to minimum free energy models and computational methods, we investigate the RNA pseudoknotted structure. The paper present 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 Pseudo Base indicate that the algorithm is more effective and precise, the algorithm can predict arbitrary pseudoknots. And the paper present a 2-approximation algorithm by analyzing the RNA folding structure, there exists 1+t (t>0) polynomial time approximation scheme in searching maximum number of stackings, and we give the proof of the approximation scheme in RNA structure.
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