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

Abstract

Background 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. These are however difficult to analyze simultaneously. Results This 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 C ircular S econdary S tructure B ase P airs P robabilities Plot ( CS 2 BP 2 -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 CS 2 BP 2 -Plots along with the traditional graph, planar and circular diagrams obtained with VARNA. The CS 2 BP 2 -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. Conclusions Using 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://nrcmonsrv01.nrc.ca/cs2bp2plot

Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts

“…To highlight the latter point further, we show in Figure 3 circular secondary structure base pair probability plots (CS 2 BP 2 Plots) 46 of four representative RNAs, namely, the core domain of the human telomerase RNA (PDB ID: 2L3E), the group II intron ai5γ RNA (PDB ID: 2LU0), the fluoride riboswitch RNA (PDB ID: 5KH8), and the TMR aptamer 3 RNA (PDB ID: 6GZK). The complete set of CS 2 BP 2 Plots can be found in the Supporting Information (Figures S4−S18).…”

“…In these plots, the RNA residues are arranged along a circle, and the base pairs are represented as lines between individual residues. To summarize the CS-BME ensembles, we used circular secondary structure base pair probability plots (CS 2 BP 2 plots), circular secondary structure plots in which base pair probability information is encoded in the color and thickness of the lines respecting base pairs. We generated these plots using in-house R-scripts.…”