Parametric analysis of RNA branching configurations

DOI10.1007/S11538-010-9607-3zbMATH Open1214.92020arXiv0904.3700OpenAlexW1976652160WikidataQ46167873 ScholiaQ46167873MaRDI QIDQ542013FDOQ542013

Authors: Valerie Hower, Christine E. Heitsch 

Publication date: 8 June 2011

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

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.

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

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

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)

Cites Work

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

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

Uses Software

• Mfold

This page was built for publication: Parametric analysis of RNA branching configurations

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q542013)