From 61aa402837621b3e80ec61d56152ea0c858b319d Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Mon, 23 May 2011 19:56:44 +0200 Subject: [PATCH] 'Add doc for JalviewRNASupport what was done/todo' merge; JAL-580 Change-Id: I01c765ad11001371129134a1b2cc35c5f44dd1af --- doc/JalviewRNASupport.html | 75 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 doc/JalviewRNASupport.html diff --git a/doc/JalviewRNASupport.html b/doc/JalviewRNASupport.html new file mode 100644 index 0000000..d96cca5 --- /dev/null +++ b/doc/JalviewRNASupport.html @@ -0,0 +1,75 @@ + + +Jalview RNA Support + +

+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

+ + + -- 1.7.10.2