-<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→Secondary Structure \r
-Prediction→Muscle Alignment </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>
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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
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+ * Jalview is free software: you can redistribute it and/or
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+ *
+ * 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>
+<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 most recent version of the method, JPred4, employs a
+ series of neural networks trained to predict different secondary
+ structure types from a sequence profile, and when necessary, employs
+ a jury network to identify the most likely secondary structure
+ prediction.<br>
+ <ul>
+ <li>Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)<br />
+ JPred4: a protein secondary structure prediction server<br /> <em>Nucleic
+ Acids Research</em>, <strong>Web Server issue</strong> (first
+ published 15th April 2015)<br /> <a
+ href="http://dx.doi.org/10.1093/nar/gkv332">http://dx.doi.org/10.1093/nar/gkv332</a>
+ </li>
+ <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>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>
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