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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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-<head><title>RNA Helices Colouring</title></head>
+ * 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.
+ -->
+<head>
+<title>RNA Helices Colouring</title>
+</head>
<body>
-<p><strong> RNA Helices Colouring </strong></p>
-<p>An RNA alignment loaded from a Stockholm file can be coloured
- based on its helices. The helices are determined from the
- secondary structure line in the Stockholm file (#GC SS_cons)
- written in WUSS notation
- that specifies base pairing. See <a href="http://en.wikipedia.org/wiki/Stockholm_format">
- Wikipedia</a> or <a href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
- Jalview RNA Support Blog</a> for more information about Stockholm files and WUSS notation.</p>
-Select "Colour" <strong>→</strong> "
- By RNA Helices" to colour the alignment by RNA helices. <br>
+ <p>
+ <strong> RNA Helices Colouring </strong>
+ </p>
+ <p>
+ An RNA alignment loaded from a Stockholm file can be coloured based
+ on its helices. The helices are determined from the secondary
+ structure line in the Stockholm file (#GC SS_cons) written in WUSS
+ notation that specifies base pairing. See <a
+ href="http://en.wikipedia.org/wiki/Stockholm_format">
+ Wikipedia</a> or <a
+ href="http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html">
+ Jalview RNA Support Blog</a> for more information about Stockholm
+ files and WUSS notation.
+ </p>
+ Select "Colour"
+ <strong>→</strong> " By RNA Helices" to colour the
+ alignment by RNA helices.
+ <br>
<br>
-<p><em>Features</em></p>
-<ul>
-<li>Colours are generated randomly for the number of helices present.
-Reselect the "By RNA Helices" option to generate another set of random colors. </li>
-<li>Sequence logo is in <a href="purinepyrimidine.html">
-Purine/Pyrimidine colour scheme</a>. </li>
-<li>Line above the "Secondary Structure" line in annotation panel is WUSS notation present
-in the input file.</li>
-</ul>
-
-
-
+ <p>
+ <em>Features</em>
+ </p>
+ <ul>
+ <li>Colours are generated randomly for the number of helices
+ present. Reselect the "By RNA Helices" option to generate another
+ set of random colors.</li>
+ <li>Sequence logo is in <a href="purinepyrimidine.html">
+ Purine/Pyrimidine colour scheme</a>.
+ </li>
+ <li>Line above the "Secondary Structure" line in annotation
+ panel is WUSS notation present in the input file.</li>
+ </ul>
+
+
+
<div align="center">
- <img src="rnahelicescoloring.png" width="600" height="140"> </div>
-
+ <img src="rnahelicescoloring.png" width="600" height="140">
+ </div>
+
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff