3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
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22 <head><title>RNA Helices Colouring</title></head>
25 <p><strong> RNA Helices Colouring </strong></p>
26 <p>An RNA alignment loaded from a Stockholm file can be coloured
27 based on its helices. The helices are determined from the
28 secondary structure line in the Stockholm file (#GC SS_cons)
29 written in WUSS notation
30 that specifies base pairing. See <a href="http://en.wikipedia.org/wiki/Stockholm_format">
31 Wikipedia</a> or <a href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
32 Jalview RNA Support Blog</a> for more information about Stockholm files and WUSS notation.</p>
33 Select "Colour" <strong>→</strong> "
34 By RNA Helices" to colour the alignment by RNA helices. <br>
36 <p><em>Features</em></p>
38 <li>Colours are generated randomly for the number of helices present.
39 Reselect the "By RNA Helices" option to generate another set of random colors. </li>
40 <li>Sequence logo is in <a href="purinepyrimidine.html">
41 Purine/Pyrimidine colour scheme</a>. </li>
42 <li>Line above the "Secondary Structure" line in annotation panel is WUSS notation present
43 in the input file.</li>
49 <img src="rnahelicescoloring.png" width="600" height="140"> </div>