3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 <head><title>RNA Helices Colouring</title></head>
22 <p><strong> RNA Helices Colouring </strong></p>
23 <p>An RNA alignment loaded from a Stockholm file can be coloured
24 based on its helices. The helices are determined from the
25 secondary structure line in the Stockholm file (#GC SS_cons)
26 written in WUSS notation
27 that specifies base pairing. See <a href="http://en.wikipedia.org/wiki/Stockholm_format">
28 Wikipedia</a> or <a href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
29 Jalview RNA Support Blog</a> for more information about Stockholm files and WUSS notation.</p>
30 Select "Colour" <strong>→</strong> "
31 By RNA Helices" to colour the alignment by RNA helices. <br>
33 <p><em>Features</em></p>
35 <li>Colours are generated randomly for the number of helices present.
36 Reselect the "By RNA Helices" option to generate another set of random colors. </li>
37 <li>Sequence logo is in <a href="purinepyrimidine.html">
38 Purine/Pyrimidine colour scheme</a>. </li>
39 <li>Line above the "Secondary Structure" line in annotation panel is WUSS notation present
40 in the input file.</li>
46 <img src="rnahelicescoloring.png" width="600" height="140"> </div>