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Properties of
RNA secondary structure matching models
Nicole Anderson, Michael Breunig, Kyle Goryl, Hannah Lewis, Manda Riehl and McKenzie Scanlan
Vol. 12 (2019), No. 2, 257–280
DOI: 10.2140/involve.2019.12.257
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Abstract |
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RNA secondary structures have been modeled using a variety of matching families. We first explore the intersections of different matching families which are models for likely RNA secondary structures. We then introduce their respective enumeration sequences and prove our proposed equations for enumeration. Next, we prove a formula for the number of matchings with a given crossing number for a variety of matching families. Then we develop a new statistic called the pseudoknot number and find the maximum pseudoknot number on a given set of matchings. We end by providing a comparison between the crossing number, nesting number, and pseudoknot number for three matching families on nine edges. |
Keywords
RNA secondary structure, perfect matchings, crossing
number, nesting number, pseudoknot
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Mathematical Subject Classification 2010
Primary: 05C30, 92E10
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Milestones
Received: 22 July 2017
Revised: 3 April 2018
Accepted: 4 April 2018
Published: 8 October 2018
Communicated by Anant Godbole
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Authors |
| Nicole Anderson | |
| University of Wisconsin Eau Claire, WI United States |
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| Michael Breunig | |
| University of Wisconsin Eau Claire, WI United States |
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| Kyle Goryl | |
| University of Wisconsin Milwaukee, WI United States |
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| Hannah Lewis | |
| University of Wisconsin Eau Claire, WI United States |
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| Manda Riehl | |
| Department of Mathematics Rose-Hulman Institute of Technology Terre Haute, IN United States |
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| McKenzie Scanlan | |
| University of Wisconsin Eau Claire, WI United States |
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