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+<head>
+<title>JPred Secondary Structure Prediction</title>
+</head>
+<body>
+ <strong>JPred 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→JPred 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 JPred 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 JPred 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 JPred 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>: JPred 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
+ JPred's own reliability score (see below).
+ </p>
+ <p>The result of a JPred 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>Jnet Burial<br> <em>Prediction of Solvent
+ Accessibility. levels are
+ <ul>
+ <li>0 - Exposed</li>
+ <li>3 - 25% or more S.A. accessible</li>
+ <li>6 - 5% or more S.A. accessible</li>
+ <li>9 - Buried (<5% exposed)</li>
+ </ul></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>JNETPSSM<br> <em>PSSM 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>JPred 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 JPred 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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