+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<title>Jalview RNA Support</title>
-<body>
-<h1>
-Jalview RNA Support
-</h1>
-<p>
-Jalview RNA support was first added during a
-<a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2010">2010 Google Summer of Code Project</a> by
-Lauren Lui (see her <a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Extending_Jalview_to_Support_RNA_Alignment_Annotation_and_Secondary_Structure_Visualization">
-NESCent wiki page</a> and the project <a href="http://jalview-rnasupport.blogspot.com/">blog</a>).
-</p>
-<h2>What was added</h2>
-<p>
-<ul>
-<li>Recognition of ".stk" and ".sto" extensions for Stockholm file format.</li>
-<li>Purine/Pyrimidine colour scheme.</li>
-<li>Colouring by RNA helices. Helices are determined from the secondary structure line written in WUSS format in Stockholm files.</li>
-<li>Ability to fetch sequences from RFAM.</li>
-<li>Visualization of RNA secondary structure in WUSS format (from input file) and RNA helices in the
-annotation panel.</li>
-</ul>
-</p>
-<p>In 2011, Jan Engelhardt was supported by <a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2011">GSOC</a> to extend Lauren's work, with <a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:_Extending_Jalview_support_for_handling_RNA">support for viewing secondary structure in VARNA and visualizing base pair contact conservation</a>.
-</p>
-<h2>What Jan added</h2>
-<p>
-<ul>
-<li>Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files</li>
-<li>Incorporated <a href="varna.lri.fr">VARNA</a> into the desktop application</li>
-<li>Added a new base pair consensus histogram and sequence logo annotation row</li>
-</ul>
-</p>
-<h2>TODO</h2>
-<h3>Secondary Structure Visualization/Annotation</h3>
-<ul>
-<li>Detection of pseudoknots and tetraloops </li>
-<li>Update colouring of RNA helices in annotation panel when "By RNA helices" colouring is selected</li>
-<li>Editing of secondary structure line</li>
-<li>Update helix colouring when secondary structure changes.</li>
-<li>Support per sequence in RNA secondary structure annotation</li>
-</ul>
-
-<h3>Colour schemes</h3>
-<ul>
-<li>Coloring scheme for pseudoknots</li>
-<li>Covariation colour scheme similar to RFAM's</li>
-<li>Coloring schemes from other MSA viewers, like 4Sale and Assemble</li>
-<li>Highlight positions in alignments that break base pairing specified in the secondary structure line</li>
-</ul>
-<h3>Embed VARNA, An RNA Secondary Structure Viewer</h3>
-<ul>
-<li>The homepage for VARNA can be found <a href="http://varna.lri.fr/">here</a>.</li>
-<li>Hook VARNA into Jalview</li>
-<li>Ability to port RNA secondary structure (e.g. from Stockholm files) into VARNA</li>
-<li>Mouse over and selections get highlighted in the linked views</li>
-</ul>
-<h3>Miscellaneous</h3>
-<ul>
-<li>Add changes done to the main gui to the applet gui</li>
-<li>Add export of Stockholm file format</li>
-</ul>
-</p>
-</body>
-</html>
-
git://source.jalview.org / jalview.git / blobdiff