Asymptotic connectivity for the network of RNA secondary structures

2015/08/16 by Peter Clote, Clote, Peter
Biochemistry, Genetics and Molecular Biology · #05A16 #Bacterial Genetics and Biotechnology #Biomolecules (q-bio.BM) #FOS: Biological sciences #RNA Research and Splicing #RNA and protein synthesis mechanisms

paper · pdf · doi:10.48550/arxiv.1508.03815

openalex publication_date 2015/08/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Given an RNA sequence a, consider the network G = (V;E), where the set V of nodes consists of all secondary structures of a, and whose edge set E consists of all edges connecting two secondary structures whose base pair distance is 1. Define the network connectivity, or expected network degree, as the average number of edges incident to vertices of G. Using algebraic combinatorial methods, we prove that the asymptotic connectivity of length n homopolymer sequences is 0:473418 ? n. This raises the question of what other network properties are characteristic of the network of RNA secondary structures. Programs in Python, C and Mathematica are available at the web site http://bioinformatics.bc.edu/clotelab/ RNAexpNumNbors.

Citations

• Singularity Analysis of Generating Functions

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