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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
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+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<title>Jalview RNA Support</title>
+<body>
+<h1>
+Jalview RNA Support
+</h1>
+<p>
+Jalview RNA support has been added in part during a
+<a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2010">Google Summer of Code Project</a>.
+More information about this project can be found at the
+<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>
+<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>
+<li>Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files</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 / commitdiff