Visualizing RNA Secondary Structure with Base Pair Binding Probabilitie

[Design Contest Entry] RNAbow diagrams are a versatile tool for visualizing and comparing ensembles of RNA secondary structures. Previously, RNAbows have proved useful when investigating individual ensembles of folds, performing cluster analysis, and identifying conformational changes caused by single nucleotide polymorphisms. This contest submission highlights their usefulness in the understanding of the effects of mutations.

The RNAbows tool provides multiple modes of use. The AllPairs method is a generalization of the rainbow diagram and represents base pair probabilities with line thickness and darkness. Because our visual processing system naturally groups parallel lines, the AllPairs method makes compatible stems easy to identify. The Difference RNAbow facilitates the comparison of the folds of different ensembles in just a glance by coloring the regions of difference. Difference RNAbows are useful when analyzing the effects of mutations, as well as comparing of clusters of structures.