Network Properties of the Ensemble of RNA Structures

• DOI: 10.1371/journal.pone.0139476
• Publication Date: 2015-10-21T17:55:54Z
• Authors: Peter Clote; Amir Bayegan
• Keywords: Degree (music); Matthews correlation coefficient

We describe the first dynamic programming algorithm that computes expected degree for network, or graph G = (V, E) of all secondary structures a given RNA sequence a1, …, an. Here, nodes V correspond to a, while an edge exists between s, t if structure can be obtained from s by adding, removing shifting base pair. Since kinetics programs implement Gillespie algorithm, which simulates random walk on network structures, may provide better understanding folding when allowing defect diffusion, helix zippering, and related conformation transformations. determine correlation degree, contact order, conformational entropy, number native contacts benchmarking dataset RNAs. Source code is available at http://bioinformatics.bc.edu/clotelab/RNAexpNumNbors.