Jalview RNA Support

Jalview RNA support has been added in part during a Google Summer of Code Project. More information about this project can be found at the 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.

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
• Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files

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