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
The R4RNA R package that R-chie uses is available for download, along the script that makes R-chie plots.
1973 seed alignments and structures from Rfam version 10.1 were downloaded from the Rfam FTP, and visualized as a covariation plot with a loop calling a function from R4RNA. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot.
The arcs are coloured by % canonical basepair of the basepaired columns in the alignment according to the Rfam consensus secondary structure. Dark blue is 100%, off-white is 50% and dark red is 0%.
Nucleotide columns in the alignment are coloured according to their basepairing status as defined by the Rfam structure. Valid basepairing columns (G:C, A:U, G:U and vice versa) are coloured green. Any valid basepair that covaries from the most commonly observed valid basepair (i.e. contains compensatory mutations to retain basepairing potential), is coloured dark blue for two-sided covariation and light blue for one-side. Invalid basepairs are coloured red. Unpaired bases are in black and gaps are in grey. Finally, any ambiguous bases (non-ACGT) or pairs with ambiguous bases are coloured purple.
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