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Entropy 2014, 16(3), 1331-1348; doi:10.3390/e16031331
Article

Describing the Structural Diversity within an RNA’s Ensemble

Received: 6 August 2013 / Revised: 15 January 2014 / Accepted: 21 February 2014 / Published: 3 March 2014
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
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Abstract: RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy and the ensemble defect. The average Shannon entropy is a measure of the structural diversity calculated from the base pair probability matrix. The ensemble defect, a tool in identifying optimal sequences for a given structure, is a measure of the average number of structural differences between a target structure and all the structures that make up the ensemble, scaled to the length of the sequence. In this paper, we show examples and discuss various uses of these metrics in both structured and unstructured RNA. By exploring how these two metrics describe RNA as an ensemble of different structures, as would be found in biological systems, it will push the field beyond the standard “structured” and “unstructured” categorization.
Keywords: secondary structure; ensemble of structures; single nucleotide polymorphisms; ribosome secondary structure; ensemble of structures; single nucleotide polymorphisms; ribosome
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Martin, J.S. Describing the Structural Diversity within an RNA’s Ensemble. Entropy 2014, 16, 1331-1348.

AMA Style

Martin JS. Describing the Structural Diversity within an RNA’s Ensemble. Entropy. 2014; 16(3):1331-1348.

Chicago/Turabian Style

Martin, Joshua S. 2014. "Describing the Structural Diversity within an RNA’s Ensemble." Entropy 16, no. 3: 1331-1348.


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