Software note: An RNA folding algorithm including pseudoknots based on dynamic weighted matching

Authors:
Haijun Liu;Dong Xu;Jianlin Shao;Yifei Wang
Affiliations:
Department of Mathematics, Shanghai University, Shanghai 200444,China;Department of Mathematics, Shanghai University, Shanghai 200444,China;College of Life Sciences, China Jiliang University, Hangzhou 310018, China;Department of Mathematics, Shanghai University, Shanghai 200444,China
Venue:
Computational Biology and Chemistry
Year:
2006

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An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

Bioinformatics

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Abstract

On the basis of maximum weighted matching (MWM) algorithm, we introduced a dynamic weight related with stem length and used a recursive algorithm to predict RNA secondary structures by searching the stem structure with maximum weight summation step-by-step. This algorithm not only avoids the complicated free energy calculation, but also it could attain higher prediction accuracy. Moreover, our algorithm can predict most types of potential pseudoknots in the RNA structure.