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Title

Algorithm for RNA Pseudoknots Prediction

Author

Hengwu li, Daming Zhu

Vol. 6  No. 1  pp. 265~272

Abstract

Pseudoknots prediction is one of the puzzles of bioinformatics. In this paper a model and its corresponding algorithm are presented, in which RNA secondary structures containing planar pseudoknots and restricted non-planar pseudoknots are represented by semi-extensible structures, extensible structures and k-stems, and are predicted with O(n4) time and O(n4) space. Compared with the Rivas algorithm of O(n6) time and O(n4) space, this algorithm has the same power for the planar pseudoknots prediction .

Keywords

RNA secondary structure, dynamic programming, thermodynamics, NP-complete

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