Visualizing RNA base-pairing probabilities with RNAbow diagrams

RNA. 2013 Apr;19(4):475-8. doi: 10.1261/rna.033365.112. Epub 2013 Feb 13.

Abstract

There are many effective ways to represent a minimum free energy RNA secondary structure that make it easy to locate its helices and loops. It is a greater challenge to visualize the thermal average probabilities of all folds in a partition function sum; dot plot representations are often puzzling. Therefore, we introduce the RNAbows visualization tool for RNA base pair probabilities. RNAbows represent base pair probabilities with line thickness and shading, yielding intuitive diagrams. RNAbows aid in disentangling incompatible structures, allow comparisons between clusters of folds, highlight differences between wild-type and mutant folds, and are also rather beautiful.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Nucleic Acid Conformation
  • RNA / chemistry*
  • RNA / genetics
  • Software*
  • Thermodynamics

Substances

  • RNA