# Jalview RNA Support

Jalview RNA support was first added during a 2010 Google Summer of Code Project by Lauren Lui (see her NESCent wiki page and the project blog).

## What was added

- Recognition of ".stk" and ".sto" extensions for Stockholm file format.
- Purine/Pyrimidine colour scheme.
- Colouring by RNA helices. Helices are determined from the secondary structure line written in WUSS format in Stockholm files.
- Ability to fetch sequences from RFAM.
- Visualization of RNA secondary structure in WUSS format (from input file) and RNA helices in the annotation panel.

In 2011, Jan Engelhardt was supported by GSOC to extend Lauren's work, with support for viewing secondary structure in VARNA and visualizing base pair contact conservation.

## What Jan added

- Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files
- Incorporated VARNA into the desktop application
- Added a new base pair consensus histogram and sequence logo annotation row

## TODO

### Secondary Structure Visualization/Annotation

- Detection of pseudoknots and tetraloops
- Update colouring of RNA helices in annotation panel when "By RNA helices" colouring is selected
- Editing of secondary structure line
- Update helix colouring when secondary structure changes.
- Support per sequence in RNA secondary structure annotation

### Colour schemes

- Coloring scheme for pseudoknots
- Covariation colour scheme similar to RFAM's
- Coloring schemes from other MSA viewers, like 4Sale and Assemble
- Highlight positions in alignments that break base pairing specified in the secondary structure line

### Embed VARNA, An RNA Secondary Structure Viewer

- The homepage for VARNA can be found here.
- Hook VARNA into Jalview
- Ability to port RNA secondary structure (e.g. from Stockholm files) into VARNA
- Mouse over and selections get highlighted in the linked views

### Miscellaneous

- Add changes done to the main gui to the applet gui
- Add export of Stockholm file format