Pairwise visual comparison of small RNA secondary structures with base pair probabilities

Serge Léger,Maria Beatriz Walter Costa,Dan Tulpan

doi:10.1186/s12859-019-2902-6

Serge Léger, Maria Beatriz Walter Costa + Show 1 more

Open Access

https://doi.org/10.1186/s12859-019-2902-6

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Abstract

BackgroundPredicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. These are however difficult to analyze simultaneously.ResultsThis work introduces a compact unified view of the most stable conformation of an RNA secondary structure and its base pair probabilities, which is called the Circular Secondary Structure Base Pairs Probabilities Plot (CS2BP2-Plot). Along with our design we provide access to a web server implementation of our solution that facilitates pairwise comparison of short RNA (and DNA) sequences up to 200 base pairs. The web server first calculates the minimum free energy secondary structure and the base pair probabilities for up to 10 RNA or DNA sequences using RNAfold and then provides a two panel comparative view that includes CS2BP2-Plots along with the traditional graph, planar and circular diagrams obtained with VARNA. The CS2BP2-Plots include highlighting of the nucleotide differences between two selected sequences using ClustalW local alignments. We also provide descriptive statistics, dot-bracket secondary structure representations and ClustalW local alignments for compared sequences.ConclusionsUsing circular diagrams and colour and weight-coded arcs, we demonstrate how a single image can replace the state-of-the-art dual representations (dot-plots and minimum free energy structures) for base-pair probabilities of RNA secondary structures while allowing efficient exploration and comparison of different RNA conformations via a web server front end. With that, we provide the community, especially the biologically oriented, with an intuitive tool for ncRNA visualization.Web-server:https://cs2bp2plot.cluster.gctools.nrc.ca/

Highlights

Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure
Single state RNA conformations can be depicted with planar graphs, linear arc diagrams and circular diagrams, based on different ways of representing the RNA backbone
Other bioinformatics tools have been recently proposed for visualization or comparison of RNA secondary structures, such as RNA-TVCurve [12] for secondary structure comparisons and TRAVeLer [13] for visualization of structures in the presence of a template. They solve different problems and require additional constraints that limit their applicability for both comparison and visualization of RNA secondary structures with base-pair probabilities, such as the need of external structure templates, as is the case of TRAVeLer. To alleviate these limitations and to propose an alternative tool that is informative and easy to use for biologists, we present the Circular Secondary Structure Base Pairs Probabilities Plot (CS2BP2-Plot) – an intuitive visual representation of an RNA secondary structure that includes all possible base pair probabilities

Summary

Introduction

Predicted RNA secondary structures are typically visualized using dot-plots for base pair binding probabilities and planar graphs for unique structures, such as the minimum free energy structure. Traditional representations of RNA secondary structures, for example (such as linear arc diagrams, circular diagrams and planar graphs), present a single state view of a structural conformation of a nucleic acid, which provide fundamental insights into the cellular function of Visualization approaches [3,4,5,6] based on predicted RNA secondary structures [7] have been developed to separately address these needs.

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