-<html>\r
-<head>\r
-<title>JNet Secondary Structure Prediction</title>\r
-</head>\r
-<body>\r
-<strong>JNet Secondary Structure Prediction</strong>\r
-<p>\r
-Secondary structure prediction methods attempts to infer the likely secondary\r
-structure for a protein based on its amino acid composition and\r
-similarity to sequences with known secondary structure. The JNet\r
-method uses several different prediction methods and decides on the\r
-most likely prediction via a jury network. <br>\r
-<ul>\r
-<li>Cuff J. A and Barton G.J (1999) Application of enhanced multiple\r
-sequence alignment profiles to improve protein secondary\r
-structure prediction <em>Proteins</em> <strong>40</strong> 502-511</li></ul>\r
-</p>\r
-The function available from the <strong>Web Service→JNet Secondary Structure \r
-Prediction→ </strong> menu does two different kinds of prediction, \r
-dependent upon the currently selected region:</p> \r
-<ul>\r
-<li>If nothing is selected, and the displayed sequences appear to\r
-be aligned, then a JNet prediction will be run for the first\r
-sequence in the alignment, using the current\r
-alignment. Otherwise the first sequence will be submitted for prediction.\r
-</li>\r
-<li>If\r
-just one sequence (or a region on one sequence) has been selected,\r
-it will be submitted to the automatic JNet prediction server\r
-for homolog detection and prediction.\r
-</li>\r
-<li>If a set of sequences are selected, and they appear to be aligned,\r
-then the alignment will be used for a Jnet prediction on the\r
-<strong>first</strong> sequence selected in the set (that is, the one\r
-that was first clicked on).\r
-</li> \r
-</ul>\r
-<p>The result of a JNet prediction for a sequence is a new annotated\r
- alignment window:</p>\r
-<img src="jnetprediction.gif">\r
-<p>\r
-The sequence for which the prediction was made is the first one in the\r
-alignment. If a sequence based prediction was made then the remaining\r
-sequences in the alignment are the aligned parts of homologs which\r
-were used to construct a sequence profile for the prediction. If the\r
-prediction was made using a multiple alignment, then the original\r
-multiple alignment will be returned, annotated with the prediction.\r
-</p>\r
-The annotation bars below the alignment are as follows:</p>\r
-<ul>\r
-<li>Lupas_21, Lupas_14, Lupas_28<br>\r
-<em>Coiled-coil predictions for the sequence. These are binary\r
-predictions for each location.</em></li>\r
-<li>JNETSOL25,JNETSOL5,JNETSOL0<br>\r
-<em>Solvent accessibility predictions - binary predictions of 25%, 5%\r
-or 0% solvent accessibility.</em></li>\r
-<li>JNetPRED<br>\r
-<em>The consensus prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>JNetCONF<br>\r
-<em>The confidence estimate for the prediction. High values mean high\r
-confidence. prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>JNetALIGN<br>\r
-<em>Alignment based prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>JNetHMM<br>\r
-<em>HMM profile based prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>jpred<br>\r
-<em>Jpred prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>JNETPSSM<br>\r
-<em>PSSM based prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>JNETFREQ<br>\r
-<em>Amino Acid frequency based prediction - helices are marked as red tubes, and\r
-sheets as dark green arrows.</em></li>\r
-<li>JNETJURY<br>\r
-<em>A '*' in this annotation indicates that the JNETJURY was invoked\r
-to rationalise significantly different primary predictions.</em></li>\r
-</ul>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<head>
+<title>JNet Secondary Structure Prediction</title>
+</head>
+<body>
+<strong>JNet Secondary Structure Prediction</strong>
+<p>Secondary structure prediction methods attempts to infer the
+likely secondary structure for a protein based on its amino acid
+composition and similarity to sequences with known secondary structure.
+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>
+</ul>
+</p>
+The function available from the
+<strong>Web Service→Secondary Structure
+Prediction→JNet Secondary Structure Prediction</strong>
+menu does two different kinds of prediction, dependent upon the
+currently selected region:
+</p>
+<ul>
+ <li>If nothing is selected, and the displayed sequences appear to
+ be aligned, then a JNet prediction will be run for the first sequence
+ in the alignment, using the current alignment. Otherwise the first
+ sequence will be submitted for prediction.</li>
+ <li>If just one sequence (or a region on one sequence) has been
+ selected, it will be submitted to the automatic JNet prediction server
+ for homolog detection and prediction.</li>
+ <li>If a set of sequences are selected, and they appear to be
+ aligned, then the alignment will be used for a Jnet prediction on the <strong>first</strong>
+ sequence selected in the set (that is, the one nearest the top of the
+ alignment window).</li>
+</ul>
+<p><strong>Note</strong>: JNet secondary structure prediction is a
+'non-column-separable' service - predictions are based on the sequence
+profile of contiguous stretches of amino-acid sequence. A prediction
+will only be made on the visible parts of a sequence (see <a
+ href="../features/hiddenRegions.html">hiding columns</a>) as if it were
+a contiguous polypeptide chain. Prediction accuracy at the hidden column
+boundaries may therefore be less than indicated by JNet's own
+reliability score (see below).</p>
+<p>The result of a JNet prediction for a sequence is a new annotated
+alignment window:</p>
+<img src="jnetprediction.gif">
+<p>The sequence for which the prediction was made is the first one
+in the alignment. If a sequence based prediction was made then the
+remaining sequences in the alignment are the aligned parts of homologs
+which were used to construct a sequence profile for the prediction. If
+the prediction was made using a multiple alignment, then the original
+multiple alignment will be returned, annotated with the prediction.</p>
+The annotation bars below the alignment are as follows:
+</p>
+<ul>
+ <li>Lupas_21, Lupas_14, Lupas_28<br>
+ <em>Coiled-coil predictions for the sequence. These are binary
+ predictions for each location.</em></li>
+ <li>JNETSOL25,JNETSOL5,JNETSOL0<br>
+ <em>Solvent accessibility predictions - binary predictions of 25%,
+ 5% or 0% solvent accessibility.</em></li>
+ <li>JNetPRED<br>
+ <em>The consensus prediction - helices are marked as red tubes,
+ and sheets as dark green arrows.</em></li>
+ <li>JNetCONF<br>
+ <em>The confidence estimate for the prediction. High values mean
+ high confidence. prediction - helices are marked as red tubes, and
+ sheets as dark green arrows.</em></li>
+ <li>JNetALIGN<br>
+ <em>Alignment based prediction - helices are marked as red tubes,
+ and sheets as dark green arrows.</em></li>
+ <li>JNetHMM<br>
+ <em>HMM profile based prediction - helices are marked as red
+ tubes, and sheets as dark green arrows.</em></li>
+ <li>jpred<br>
+ <em>Jpred prediction - helices are marked as red tubes, and sheets
+ as dark green arrows.</em></li>
+ <li>JNETPSSM<br>
+ <em>PSSM based prediction - helices are marked as red tubes, and
+ sheets as dark green arrows.</em></li>
+ <li>JNETFREQ<br>
+ <em>Amino Acid frequency based prediction - helices are marked as
+ red tubes, and sheets as dark green arrows.</em></li>
+ <li>JNETJURY<br>
+ <em>A '*' in this annotation indicates that the JNETJURY was
+ invoked to rationalise significantly different primary predictions.</em></li>
+</ul>
+</p>
+<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
+JABAWS Jnet service.</em>
+
+</body>
+</html>
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