Degree Name

MS (Master of Science)

Program

Mathematical Sciences

Date of Award

5-2011

Committee Chair or Co-Chairs

Debra J. Knisley

Committee Members

Teresa W. Haynes, Jeff R. Knisley

Abstract

The secondary structures of ribonucleic acid (RNA) have been successfully modeled with graph-theoretic structures. Often, simple graphs are used to represent secondary RNA structures; however, in this research, a multigraph representation of RNA is used, in which vertices represent stems and edges represent the internal motifs. Any type of RNA secondary structure may be represented by a graph in this manner. We define novel graphical invariants to quantify the multigraphs and obtain characteristic descriptors of the secondary structures. These descriptors are used to train an artificial neural network (ANN) to recognize the characteristics of secondary RNA structure. Using the ANN, we classify the multigraphs as either RNA-like or not RNA-like. This classification method produced results similar to other classification methods. Given the expanding library of secondary RNA motifs, this method may provide a tool to help identify new structures and to guide the rational design of RNA molecules.

Document Type

Thesis - Open Access

Copyright

Copyright by the authors.

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