X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=doc%2FJalviewRNASupport.html;fp=doc%2FJalviewRNASupport.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=4c0500a1762a78d11d1514e968dbcb9998d56e93;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/doc/JalviewRNASupport.html b/doc/JalviewRNASupport.html deleted file mode 100644 index 4c0500a..0000000 --- a/doc/JalviewRNASupport.html +++ /dev/null @@ -1,84 +0,0 @@ - - -Jalview RNA Support - -

-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

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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

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