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Updated: May 21, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
The 5'-3' distance of RNA secondary structures
Hillary S W Han1, Christian M Reidys
1Institut for Matematik og Datalogi, University of Southern Denmark, Odense, Denmark.
Abstract:
Recently, Yoffe and colleagues observed that the average distances between 5'-3' ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical arguments maximizing certain entropy functionals. In this article, we compute the exact distribution of 5'-3' distances of RNA secondary structures for any finite n. Furthermore, we compute the limit distribution and show that for n = 30 the exact distribution and the limit distribution are very close. Our results show that the distances of random RNA secondary structures are distinctively lower than those of minimum free energy structures of random RNA sequences.
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