R-chie allows you to make arc diagrams of RNA secondary
structures, allowing for easy comparison and overlap of two
structures, rank and display basepairs in colour and to also
visualize corresponding multiple sequence alignments and
R4RNA is the R package powering R-chie, available for download and local use for more customized figures and scripting.
Visualize complicated basepairing as arcs on a linear sequence, colouring basepairs by value.
e.g. TRANSAT basepairs predictions for the Cripavirus internal ribosomal entry site (IRES), RF00458, coloured by p-value.
Plot two structures on the same sequence for easy comparison.
Top: Helices predicted by TRANSAT for the Cripavirus IRES, RF00458, coloured by p-value.
Bottom: Helices known from experimentally determined structure.