Vol. 12, No. 2, 2019

Download this article
Download this article For screen
For printing
Recent Issues

Volume 12
Issue 2, 181–360
Issue 1, 1–180

Volume 11, 5 issues

Volume 10, 5 issues

Volume 9, 5 issues

Volume 8, 5 issues

Volume 7, 6 issues

Volume 6, 4 issues

Volume 5, 4 issues

Volume 4, 4 issues

Volume 3, 4 issues

Volume 2, 5 issues

Volume 1, 2 issues

The Journal
About the Journal
Subscriptions
Editorial Board
Editors’ Interests
Scientific Advantages
Submission Guidelines
Submission Form
Ethics Statement
Editorial Login
Author Index
Coming Soon
Contacts
 
ISSN: 1944-4184 (e-only)
ISSN: 1944-4176 (print)
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
Abstract

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
Mathematical Subject Classification 2010
Primary: 05C30, 92E10
Milestones
Received: 22 July 2017
Revised: 3 April 2018
Accepted: 4 April 2018
Published: 8 October 2018

Communicated by Anant Godbole
Authors
Nicole Anderson
University of Wisconsin
Eau Claire, WI
United States
Michael Breunig
University of Wisconsin
Eau Claire, WI
United States
Kyle Goryl
University of Wisconsin
Milwaukee, WI
United States
Hannah Lewis
University of Wisconsin
Eau Claire, WI
United States
Manda Riehl
Department of Mathematics
Rose-Hulman Institute of Technology
Terre Haute, IN
United States
McKenzie Scanlan
University of Wisconsin
Eau Claire, WI
United States