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Updated: May 16, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA
Amirhossein Manzourolajdad1, Yingfeng Wang, Timothy I Shaw
1Institute of Bioinformatics, University of Georgia, Davison Life Sciences Bldg, Room B118B, 120 Green St, Athens, GA 30602, USA. amanzour@uga.edu
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RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon's entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon's entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families.
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URL http://www.plantbio.uga.edu/~russell/index.php?s=1&n=5&r=0.
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