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Using folding ensemble and stem probability maximization methods to predict RNA H-type pseudoknots

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3 Author(s)
Spirollari, Junilda ; Bioinformatics Program, Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA ; Wang, Shawn Xiong ; Wang, Jason T.L.

We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by utilizing a search technique with a pseudo-probability scoring scheme. Experimental results show that KnotFold achieves higher sensitivity than existing methods. The KnotFold package with documentation is freely available at

Published in:

Tsinghua Science and Technology  (Volume:17 ,  Issue: 6 )