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

DOI10.1016/J.DAM.2005.04.022zbMATH Open1108.92016OpenAlexW2112945167MaRDI QIDQ876474FDOQ876474

D. Krizanc, Evangelos Kranakis, 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

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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)

Cites Work

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• Investigation of the Bernoulli model for RNA secondary structures
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• Longest common subsequences
• Subadditive ergodic theory
• Longest common subsequences of two random sequences
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• On some new sequences generalizing the Catalan and Motzkin numbers
• Combinatorics of RNA secondary structures
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Cited In (7)

• On the problem of reconstructing a mixture of \textsc{rna} structures
• Asymptotics for local maximal stack scores with general loop penalty function
• Fast string matching by using probabilities: on an optimal mismatch variant of Horspool's algorithm
• Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding
• Large deviations for random trees and the branching of RNA secondary structures
• Random words in free groups, non-crossing matchings and RNA secondary structures
• A semi-bijective algorithm for saturated extended 2-regular simple stacks

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