R-chie [ɑrči]
A web server and R package for plotting arc diagrams of RNA secondary structures

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 co-variation information.
R4RNA is the R package powering R-chie, available for download and local use for more customized figures and scripting.

Available types of plots (click to load example input to web form)

Single structure arc diagram

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.

Double structure arc diagram

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.

Overlapping structure arc diagram
Overlap two structures to highlight similarities and differences on the same sequence.
Top: The known reference structure of RF00458, coloured by p-values when predicted by TRANSAT.
Bottom: TRANSAT predicted helices not found in the known structure, coloured by p-value.
Single structure covariance arc diagram
Display multiple sequence alignments with structure, colouring alignment nucleotides by basepair status.
e.g. Rfam Basepairs for RF00458 coloured by covariation, over alignment of seven homologues coloured by basepairing status.
Double structure covariance arc diagram
Display multiple sequence alignments for two structures for easy comparison of structures and/or alignments.
Top: Rfam structure for Cripavirus IRES, RF00458, coloured by conservation, on top of an alignment of homologues.
Bottom: Predicted structure of RF00458 coloured by percent canonical basepairs, below the same alignment
Overlapping structure covariance arc diagram
Highlight similarities and differences of two structures using basepair information for known and novel basepairs on alignments.
Top: Known RF00458 helices, shown in colour when predicted by TRANSAT, with covariance of predicted helices.
Bottom: Novel helices predicted by TRANSAT in RF00458, coloured by scored, showing covariation.