RNA Helices Colouring

RNA Helices Colouring

An RNA alignment loaded from a Stockholm file can be coloured based on its helices. The helices are determined from the secondary structure line in the Stockholm file (#GC SS_cons) written in WUSS notation that specifies base pairing. See Wikipedia or Jalview RNA Support Blog for more information about Stockholm files and WUSS notation.

Select "Colour" → " By RNA Helices" to colour the alignment by RNA helices.

Features

Colours are generated randomly for the number of helices present. Reselect the "By RNA Helices" option to generate another set of random colors.
Sequence logo is in Purine/Pyrimidine colour scheme.
Line above the "Secondary Structure" line in annotation panel is WUSS notation present in the input file.