A new pseudoknots folding algorithm for RNA structure prediction

Authors:
Hengwu Li;Daming Zhu
Affiliations:
School of Computer Sci and Tech, Shan Dong Univ, Jinan, P.R. China;School of Computer Sci and Tech, Shan Dong Univ, Jinan, P.R. China
Venue:
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Year:
2005

Citing 2
Cited 0

Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

Discrete Applied Mathematics - Special volume on combinatorial molecular biology
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

Bioinformatics

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Abstract

A new dynamic programming algorithm with O(n4) time and O(n3) space is presented to predict the RNA secondary structure including nested pseudoknots and a subclass of crossed pseudoknots. Compared with the Jens algorithm of O(n4) time and O(n2) space, this algorithm can predict more complex pseudoknots. Compared with the Rivas algorithm of O(n6) time and O(n4) space, this algorithm has the same power for the planar pseudoknots prediction.