An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots

Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base‐pairing probabilities starting from the output of this partition functi...

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Bibliographic Details
Published in:Journal of computational chemistry 2004-07, Vol.25 (10), p.1295-1304
Main Authors: Dirks, Robert M., Pierce, Niles A.
Format: Article
Language:English
Subjects:
Acids
Algorithms
Base Sequence
base-pairing probabilities
Computational Biology
Computers
DNA
DNA - chemistry
Humans
Models, Molecular
Nucleic Acid Conformation
partition function
Probability
pseudoknots
RNA
RNA - chemistry
Telomerase - chemistry
Thermodynamics
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Summary:Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base‐pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base‐pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1295–1304, 2004
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.20057