Volume 6 Number 2 (Feb. 2011)
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JSW 2011 Vol.6(2): 233-240 ISSN: 1796-217X
doi: 10.4304/jsw.6.2.233-240

Approximation Algorithm and Scheme for RNA Maximum Weighted Stacking

Hengwu Li, Huijian Han, Zhenzhong Xu
School of Computer Science and Technology, Shandong Economic University, Jinan, China

Abstract—Pseudoknotted RNA structure prediction is an important problem in bioinformatics. Existing polynomial time algorithms have no performance guarantee or can handle only limited types of pseudoknots. In this paper for the general problem of pseudoknotted RNA structure prediction, maximum weighted stacking problem is presented based on stacking actions, and its polynomial time approximation algorithm with O(nlogn) time and O(n) space and polynomial time approximation scheme are given. The approximate performance ratio of this approximation algorithm is 3. Compared with existing polynomial time algorithm, they have exact approximation performance and can predict arbitrary pseudoknots.

Index Terms—RNA structure, appproximation algorithm, approximation scheme, pseudoknot

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Cite: Hengwu Li, Huijian Han, Zhenzhong Xu, "Approximation Algorithm and Scheme for RNA Maximum Weighted Stacking," Journal of Software vol. 6, no. 2, pp. 233-240, 2011.

General Information

ISSN: 1796-217X (Online)
Frequency:  Quarterly
Editor-in-Chief: Prof. Antanas Verikas
Executive Editor: Ms. Yoyo Y. Zhou
Abstracting/ Indexing: DBLP, EBSCO, CNKIGoogle Scholar, ProQuest, INSPEC(IET), ULRICH's Periodicals Directory, WorldCat, etc
E-mail: jsw@iap.org
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