<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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.
+ *
+ * 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>JNet Secondary Structure Prediction</title>
</head>
The JNet method uses several different neural networks and decides on
the most likely prediction via a jury network. <br>
<ul>
+ <li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
+ secondary structure prediction server <em>Nucleic Acids Research</em> <strong>36</strong>
+ W197-W201</li>
<li>Cuff J. A and Barton G.J (1999) Application of enhanced
multiple sequence alignment profiles to improve protein secondary
structure prediction <em>Proteins</em> <strong>40</strong> 502-511</li>
invoked to rationalise significantly different primary predictions.</em></li>
</ul>
</p>
+ <em>JNet annotation created in Jalview 2.8.2 and later versions
+ can be displayed on other alignments via the <a
+ href="../features/annotation.html#seqannots">Add reference
+ annotation</a> Sequence ID popup menu option.
+ </em>
+ <em>As of Jalview 2.6, the Jnet service accessed accessed via the
+'Secondary structure prediction' submenu should be considered a legacy
+Jalview SOAP service, and will be replaced in the near future by a
+JPred4 Rest service.</em>
+
</body>
</html>