The Circular Secondary Structure Uncertainty Plot (CS2-UPlot) - Visualizing RNA Secondary Structure with Base Pair Binding Probabilities

Dan Tulpan

[Design Contest Entry]  The Circular Secondary Structure Uncertainty Plot (CS2-UPlot) 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 is comprised of 3 concentric graphical layers representing the three main information components of an RNA secondary structure required by the BioVis 2015 Design challenge: (i) the RNA sequence (outer layer), (ii) uncertainty and free energy (mfe) scatter plots for each base (middle layer) and, (iii) uncertainty and minimum free energy (mfe) base pairings (inner layer). The CS2-UPlot challenges the classical ways of representing RNA secondary structures and combines base pairings with dot-plot values in a single graphical representation capable of assisting biologists to quickly identify similarities and differences among a large number of secondary structures and their corresponding RNA sequences. Availability: Figures can be downloaded from:    

BioVis 2015 Information