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.