The CS2-Uplot

The Circular Secondary Structure Uncertainity Plot is an intuitive visual representation of an RNA secondary structure that includes the uncertainty of all possible base pairings. The CS2-Uplot uses a chord diagram layout and consists of 3 concentric graphical layers representing the 3 main information components of an RNA secondary structure required by the BioVis 2015 Design Challenge: (i) the RNA sequence, (ii) uncertainty and free energy scatter plots for each base, and (iii) uncertainty and minimum free energy base pairings.

Below we provide examples of CS2-Uplot for the three data sets provided by the BioVis 2015 Design Challenge.

Denisovan [.png] Ancestral chimp [.png] Human [.png]

The color palette of the chords is proportional with the uncertainty level corresponding to each base pair. The most stable base pairs are colored in red and together form the MFE structure. The stability decreases as the color transitions from red (most stable) to blue (least stable) via orange and green shades.

For more information regarding this type of secondary structure representation contact Dan Tulpan.


D. Tulpan (2015). The Circular Secondary Structure Uncertainty Plot (CS 2 -UPlot) - Visualizing RNA Secondary Structure with Base Pair Binding Probabilities. The 5th Symposium on Biological Data Visualization (BioVis 2015), July 10-11, 2015, Dublin, Ireland. (pdf)