3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <title>Jalview RNA Support</title>
25 Jalview RNA support has been added in part during a
26 <a href="http://socghop.appspot.com/gsoc/program/home/google/gsoc2010">Google Summer of Code Project</a>.
27 More information about this project can be found at the
28 <a href="https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Extending_Jalview_to_Support_RNA_Alignment_Annotation_and_Secondary_Structure_Visualization">
29 NESCent wiki page</a> and the project <a href="http://jalview-rnasupport.blogspot.com/">blog</a>.
31 <h2>What was added</h2>
34 <li>Recognition of ".stk" and ".sto" extensions for Stockholm file format.</li>
35 <li>Purine/Pyrimidine colour scheme.</li>
36 <li>Colouring by RNA helices. Helices are determined from the secondary structure line written in WUSS format in Stockholm files.</li>
37 <li>Ability to fetch sequences from RFAM.</li>
38 <li>Visualization of RNA secondary structure in WUSS format (from input file) and RNA helices in the
39 annotation panel.</li>
43 <h3>Secondary Structure Visualization/Annotation</h3>
45 <li>Detection of pseudoknots and tetraloops </li>
46 <li>Update colouring of RNA helices in annotation panel when "By RNA helices" colouring is selected</li>
47 <li>Editing of secondary structure line</li>
48 <li>Update helix colouring when secondary structure changes.</li>
49 <li>Support per sequence in RNA secondary structure annotation</li>
50 <li>Enable RNA secondary structure annotation to be imported/exported through Jalview annotation files</li>
53 <h3>Colour schemes</h3>
55 <li>Coloring scheme for pseudoknots</li>
56 <li>Covariation colour scheme similar to RFAM's</li>
57 <li>Coloring schemes from other MSA viewers, like 4Sale and Assemble</li>
58 <li>Highlight positions in alignments that break base pairing specified in the secondary structure line</li>
60 <h3>Embed VARNA, An RNA Secondary Structure Viewer</h3>
62 <li>The homepage for VARNA can be found <a href="http://varna.lri.fr/">here</a>.</li>
63 <li>Hook VARNA into Jalview</li>
64 <li>Ability to port RNA secondary structure (e.g. from Stockholm files) into VARNA</li>
65 <li>Mouse over and selections get highlighted in the linked views</li>
67 <h3>Miscellaneous</h3>
69 <li>Add changes done to the main gui to the applet gui</li>
70 <li>Add export of Stockholm file format</li>