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Related Experiment Video

Updated: Feb 18, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

Aleksandar Spasic^1,2, Sarah M Assmann³, Philip C Bevilacqua⁴

¹Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.

Nucleic Acids Research

|November 28, 2017

Summary

This summary is machine-generated.

This study introduces Rsample, a new algorithm for RNA structure prediction. Rsample accurately models multiple RNA structures and their probabilities, improving upon methods that assume a single structure.

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Area of Science:

Computational Biology
Molecular Biology
Bioinformatics

Background:

RNA secondary structure prediction is crucial for understanding RNA function.
Experimental mapping data, like SHAPE, enhance prediction accuracy by revealing nucleotide pairing status.
Existing methods often assume RNAs adopt a single structure, limiting accuracy for RNAs with multiple conformations.

Purpose of the Study:

To develop an algorithm, Rsample, that predicts multiple RNA structures and their equilibrium probabilities.
To overcome the limitations of single-structure prediction models for RNAs that exist in multiple conformations.

Main Methods:

Developed the Rsample algorithm for RNA secondary structure prediction.
Utilized experimental SHAPE mapping data to inform predictions.
Modeled ensembles of RNA structures and their relative probabilities.

Main Results:

Rsample accurately predicts multiple RNA structures for sequences.
The algorithm successfully models the relative probabilities of these co-existing structures.
Demonstrated improved RNA structure modeling using SHAPE data.

Conclusions:

Rsample advances RNA structure prediction by accounting for conformational heterogeneity.
Accurate modeling of multiple RNA structures and their probabilities is achievable.
The Rsample algorithm is available within the RNAstructure software package.