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Updated: Jun 8, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Shapes of RNA pseudoknot structures
Christian M Reidys1, Rita R Wang
1Center for Combinatorics, LPMC-TJKLC, Nankai University, Tianjin, PR China. duck@santafe.edu
Abstract:
In this article, we study abstract shapes of k-noncrossing, σ-canonical RNA pseudoknot structures. We consider lv1k- and lv5k-shapes, which represent a generalization of the abstract π'- and π-shapes of RNA secondary structures introduced by Giegerich et al. Using a novel approach, we compute the generating functions of lv1k- and lv5k-shapes as well as the generating functions of all lv1k- and lv5k-shapes induced by all k-noncrossing, σ-canonical RNA structures for fixed n. By means of singularity analysis of the generating functions, we derive explicit asymptotic expressions For online Supplementary Material, see www.liebertonline.com.
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