Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov-Jacobson energy model

Authors:
Peter Clote;Evangelos Kranakis;Danny Krizanc;Ladislav Stacho
Affiliations:
Department of Biology (courtesy), Higgins Hall 355, Boston College, Chestnut Hill, MA 02467, USA and Department of Computer Science, Higgins Hall 355, Boston College, Chestnut Hill, MA 02467, USA;School of Computer Science, Carleton University, Ottawa, Ont., Canada K1S 5B6;Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA;Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Venue:
Discrete Applied Mathematics
Year:
2007

Citing 4
Cited 0

Randomized algorithms

Randomized algorithms
Combinatorics of RNA secondary structures

Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
Longest Common Subsequences

MFCS '94 Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences

Bioinformatics

Quantified Score

Hi-index	0.04

Visualization

Abstract

Motivated by computer experiments, we study asymptotics of the expected maximum number of base pairs in secondary structures for random RNA sequences of length n. After proving a general limit result, we provide estimates of the limit for the binary alphabet {G,C} with thresholds k=0. We prove a general theorem entailing the existence of an asymptotic limit for the mean and standard deviation of free energy per nucleotide, as computed by mfold, for random RNA of any fixed compositional frequency; higher order moment limits are additionally shown to exist.