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