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Title: Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs
Authors: Ieong, S.
Kao, M.-Y.
Lam, T.-W.
Sung, W.-K. 
Yiu, S.-M.
Keywords: Approximation algorithms
Computational complexity
RNA secondary structures
Stacking pairs
Issue Date: 2003
Citation: Ieong, S., Kao, M.-Y., Lam, T.-W., Sung, W.-K., Yiu, S.-M. (2003). Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs. Journal of Computational Biology 10 (6) : 981-995. ScholarBank@NUS Repository.
Abstract: The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no performance guarantee and can handle only limited types of pseudoknots. In this paper, we initiate the study of predicting RNA secondary structures with a maximum number of stacking pairs while allowing arbitrary pseudoknots. We obtain two approximation algorithms with worst-case approximation ratios of 1/2 and 1/3 for planar and general secondary structures, respectively. For an RNA sequence of n bases, the approximation algorithm for planar secondary structures runs in O(n3) time while that for the general case runs in linear time. Furthermore, we prove that allowing pseudoknots makes it NP-hard to maximize the number of stacking pairs in a planar secondary structure. This result is in contrast with the recent NP-hard results on psuedoknots which are based on optimizing some general and complicated energy functions.
Source Title: Journal of Computational Biology
ISSN: 10665277
DOI: 10.1089/106652703322756186
Appears in Collections:Staff Publications

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