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

DOI10.1016/J.DAM.2005.04.022MaRDI QIDQ876474zbMATH OpenOpenAlexFDO

Authors Evangelos Kranakis, D. Krizanc, Ladislav Stacho, Peter Clote

Publication date 18 April 2007

Published in Discrete Applied Mathematics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.dam.2005.04.022

zbMATH Keywords

secondary structureasymptotic Z-scoreNussinov-Jacobson algorithmrandom RNAZuker algorithm

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

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• Combinatorics of RNA secondary structures
• Investigation of the Bernoulli model for RNA secondary structures
• Longest common subsequences
• Longest common subsequences of two random sequences
• On some new sequences generalizing the Catalan and Motzkin numbers
• Subadditive ergodic theory

Cited in

(16)

• Asymptotics for local maximal stack scores with general loop penalty function
• Expected distance between terminal nucleotides of RNA secondary structures
• On the problem of reconstructing a mixture of \textsc{rna} structures
• A semi-bijective algorithm for saturated extended 2-regular simple stacks
• Energy and structural analysis of double nucleic acid triplets
• Fast string matching by using probabilities: on an optimal mismatch variant of Horspool's algorithm
• The expected order of saturated RNA secondary structures
• Large deviations for random trees and the branching of RNA secondary structures
• Non-crossing matchings
• Investigation of the Bernoulli model for RNA secondary structures
• Asymptotic number of hairpins of saturated RNA secondary structures
• Moments of the Boltzmann distribution for RNA secondary structures
• Random words in free groups, non-crossing matchings and RNA secondary structures
• The end-to-end distance of RNA as a randomly self-paired polymer
• The rainbow spectrum of RNA secondary structures
• Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding

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