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<head>
<title>JNet Secondary Structure Prediction</title>
</head>
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<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
+<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>
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>
+
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