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<head>
-<title>JNet Secondary Structure Prediction</title>
+<title>JPred Secondary Structure Prediction</title>
</head>
<body>
- <strong>JNet Secondary Structure Prediction</strong>
+ <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
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>
+ 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
</p>
The function available from the
<strong>Web Service→Secondary Structure
- Prediction→JNet Secondary Structure Prediction</strong> menu does two
+ 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 JNet prediction will be run for the first
+ 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 JNet prediction
+ 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 Jnet prediction on
+ 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>: JNet secondary structure prediction is a
+ <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
- JNet's own reliability score (see below).
+ JPred's own reliability score (see below).
</p>
- <p>The result of a JNet prediction for a sequence is a new
+ <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
<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>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>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
+ <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.
+ 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
+ <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>