Parametric analysis of RNA branching configurations

DOI10.1007/S11538-010-9607-3MaRDI QIDQ542013zbMATH OpenOpenAlexWikidataFDO

Authors Valerie Hower, Christine E. Heitsch

Publication date 8 June 2011

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NonCommercial 4.0 International

Full work available at URL https://arxiv.org/abs/0904.3700

zbMATH Keywords

free energyplane treethermodynamic modelparametric analysisRNA secondary structure

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Combinatorial properties of polytopes and polyhedra (number of faces, shortest paths, etc.) (52B05)

Abstract: We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy model that are not determined experimentally. Our results indicate that variation of these specific parameters does not have a dramatic effect on the structures predicted by the free energy model. We additionally map a collection of known RNA secondary structures to the RNA polytope.

Recommendations

• On the structure of RNA branching polytopes
• On a barrier height problem for RNA branching
• Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences
• Unified approach to partition functions of RNA secondary structures
• Statistics of topological RNA structures
• RNA secondary structure, permutations, and statistics
• Combinatorial analysis of interacting RNA molecules

Cites work

• An Exploration of Pick's Theorem in Space
• Enumerations of ordered trees
• Large deviations for random trees
• Large deviations for random trees and the branching of RNA secondary structures
• Linear trees and RNA secondary structure
• Ordered trees with prescribed root degrees, node degrees, and branch lengths
• Parametric Sequence Alignment
• Parametric inference for biological sequence analysis
• Parametric optimization of sequence alignment
• Tropical geometry of statistical models

Cited in

(5)

• Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences
• On the structure of RNA branching polytopes
• Optimality regions and fluctuations for Bernoulli last passage models
• Algebraic methods in mathematical biology
• Energy and structural analysis of double nucleic acid triplets

Describes a project that uses

Uses Software

• Mfold

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