Title :
An Approximation Scheme for RNA Folding Structure Prediction Including Pseudoknots
Author :
Zhendong Liu ; Daming Zhu ; Wei Cui ; Nan Liu
Author_Institution :
Sch. of Comput. Sci. & Technol., Shandong Univ., Jinan, China
Abstract :
The paper further investigates the computational problem and complexity of predicting Ribonucleic Acid structure. In order to find a way to optimize the Ribonucleic Acid pseudoknotted structure, we investigate the Ribonucleic Acid pseudoknotted structure based on thermal dynamic model, computational methods, minimum free energy are adopted to predict Ribonucleic Acid structure. The contribution of this paper is to obtain an efficient Approximation algorithm for finding RNA pseudoknotted structure, compared with other algorithms, the algorithm takes O(n3) time and O(n2) space. The experimental test in PseudoBase shows that the algorithm is more effective and exact than other algorithms, and the algorithm can predict arbitrary pseudoknots. And we also give a proof of existing 1+e (e>0) Polynomial Time Approximation Scheme(PTAS) in Searching Maximum Number of Stackings.
Keywords :
RNA; approximation theory; biocomputing; computational complexity; search problems; 1+e (e>0) polynomial time approximation scheme; PTAS; PseudoBase; RNA folding structure prediction; computational complexity; computational methods; computational problem; maximum stacking number searching; minimum free energy; ribonucleic acid pseudoknotted structure optimization; ribonucleic acid structure prediction; thermal dynamic model; Algorithm design and analysis; Approximation algorithms; Approximation methods; Heuristic algorithms; Polynomials; Prediction algorithms; RNA; Polynomial Time Approximation Schem; minimum free energy; pseudoknotted structure; stacking; stem;
Conference_Titel :
Computational Intelligence and Security (CIS), 2013 9th International Conference on
Conference_Location :
Leshan
Print_ISBN :
978-1-4799-2548-3
