Markov Chain-Based Sampling for Exploring RNA Secondary Structure under the Nearest Neighbor Thermodynamic Model and Extended Applications

ABSTRACT: Ribonucleic acid (RNA) secondary structures and branching properties are important for determining functional ramifications in biology. While energy minimization of the Nearest Neighbor Thermodynamic Model (NNTM) is commonly used to identify such properties (number of hairpins, maximum ladder distance, etc.), it is difficult to know whether the resultant values fall within expected dispersion thresholds for a given energy function. The goal of this study was to construct a Markov chain capable of examining the dispersion of RNA secondary structures and branching properties obtained from NNTM energy function minimization independent of a specific nucleotide sequence. Plane trees are studied as a model for RNA secondary structure, with energy assigned to each tree based on the NNTM, and a co

SUBMITTER: Kirkpatrick A 

PROVIDER: S-EPMC9344895 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature