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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>
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