3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>JPred Secondary Structure Prediction</title>
26 <strong>JPred Secondary Structure Prediction</strong>
28 Secondary structure prediction methods attempts to infer the likely
29 secondary structure for a protein based on its amino acid
30 composition and similarity to sequences with known secondary
31 structure. The most recent version of the method, JPred4, employs a
32 series of neural networks trained to predict different secondary
33 structure types from a sequence profile, and when necessary, employs
34 a jury network to identify the most likely secondary structure
37 <li>Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)<br />
38 JPred4: a protein secondary structure prediction server<br /> <em>Nucleic
39 Acids Research</em>, <strong>Web Server issue</strong> (first
40 published 15th April 2015)<br /> <a
41 href="http://dx.doi.org/10.1093/nar/gkv332">http://dx.doi.org/10.1093/nar/gkv332</a>
43 <li>Cole C., Barber J.D. and Barton G.J. (2008) The Jpred 3
44 secondary structure prediction server <em>Nucleic Acids
45 Research</em> <strong>36</strong> W197-W201
47 <li>Cuff J. A and Barton G.J (1999) Application of enhanced
48 multiple sequence alignment profiles to improve protein secondary
49 structure prediction <em>Proteins</em> <strong>40</strong> 502-511
53 The function available from the
54 <strong>Web Service→Secondary Structure
55 Prediction→JPred Secondary Structure Prediction</strong> menu does two
56 different kinds of prediction, dependent upon the currently selected
60 <li>If nothing is selected, and the displayed sequences appear
61 to be aligned, then a JPred prediction will be run for the first
62 sequence in the alignment, using the current alignment. Otherwise
63 the first sequence will be submitted for prediction.</li>
64 <li>If just one sequence (or a region on one sequence) has been
65 selected, it will be submitted to the automatic JPred prediction
66 server for homolog detection and prediction.</li>
67 <li>If a set of sequences are selected, and they appear to be
68 aligned, then the alignment will be used for a JPred prediction on
69 the <strong>first</strong> sequence selected in the set (that is,
70 the one nearest the top of the alignment window).
74 <strong>Note</strong>: JPred secondary structure prediction is a
75 'non-column-separable' service - predictions are based on the
76 sequence profile of contiguous stretches of amino-acid sequence. A
77 prediction will only be made on the visible parts of a sequence (see
78 <a href="../features/hiddenRegions.html">hiding columns</a>) as if
79 it were a contiguous polypeptide chain. Prediction accuracy at the
80 hidden column boundaries may therefore be less than indicated by
81 JPred's own reliability score (see below).
83 <p>The result of a JPred prediction for a sequence is a new
84 annotated alignment window:</p>
85 <img src="jnetprediction.gif">
86 <p>The sequence for which the prediction was made is the first one
87 in the alignment. If a sequence based prediction was made then the
88 remaining sequences in the alignment are the aligned parts of
89 homologs which were used to construct a sequence profile for the
90 prediction. If the prediction was made using a multiple alignment,
91 then the original multiple alignment will be returned, annotated
92 with the prediction.</p>
93 The annotation bars below the alignment are as follows:
96 <li>Lupas_21, Lupas_14, Lupas_28<br> <em>Coiled-coil
97 predictions for the sequence. These are binary predictions for
98 each location.</em></li>
99 <li>Jnet Burial<br> <em>Prediction of Solvent
100 Accessibility. levels are
103 <li>3 - 25% or more S.A. accessible</li>
104 <li>6 - 5% or more S.A. accessible</li>
105 <li>9 - Buried (<5% exposed)</li>
107 <li>JNetPRED<br> <em>The consensus prediction -
108 helices are marked as red tubes, and sheets as dark green
110 <li>JNetCONF<br> <em>The confidence estimate for the
111 prediction. High values mean high confidence. prediction -
112 helices are marked as red tubes, and sheets as dark green
114 <li>JNetALIGN<br> <em>Alignment based prediction -
115 helices are marked as red tubes, and sheets as dark green
117 <li>JNetHMM<br> <em>HMM profile based prediction -
118 helices are marked as red tubes, and sheets as dark green
120 <li>JNETPSSM<br> <em>PSSM based prediction - helices
121 are marked as red tubes, and sheets as dark green arrows.</em></li>
122 <li>JNETJURY<br> <em>A '*' in this annotation
123 indicates that the JNETJURY was invoked to rationalise
124 significantly different primary predictions.</em></li>
127 <em>JPred annotation created in Jalview 2.8.2 and later versions
128 can be displayed on other alignments via the <a
129 href="../features/annotation.html#seqannots">Add reference
130 annotation</a> Sequence ID popup menu option.
132 <em>As of Jalview 2.6, the JPred service accessed accessed via
133 the 'Secondary structure prediction' submenu should be considered a
134 legacy Jalview SOAP service, and will be replaced in the near future
135 by a JPred4 Rest service.</em>