* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<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
</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
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.
</em>
- <em>As of Jalview 2.6, the Jnet service accessed accessed via the
+ <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>
git://source.jalview.org / jalview.git / blobdiff