1 #-------------------------------------------------------------------------------
2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
5 # This file is part of Jalview.
7 # Jalview is free software: you can redistribute it and/or
8 # modify it under the terms of the GNU General Public License
9 # as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 # Jalview is distributed in the hope that it will be useful, but
12 # WITHOUT ANY WARRANTY; without even the implied warranty
13 # of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 # PURPOSE. See the GNU General Public License for more details.
16 # You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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20 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
21 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
23 * This file is part of Jalview.
25 * Jalview is free software: you can redistribute it and/or
26 * modify it under the terms of the GNU General Public License
27 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
29 * Jalview is distributed in the hope that it will be useful, but
30 * WITHOUT ANY WARRANTY; without even the implied warranty
31 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
32 * PURPOSE. See the GNU General Public License for more details.
34 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
36 <head><title>Web Service Menu</title></head>
39 <p><strong>Web Service Menu</strong></p>
41 <li><strong>Fetch DB References</strong><br>
42 <em>This will use any of the database services that Jalview is aware
43 of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
44 to verify the sequence and retrieve all database cross references and PDB ids
45 associated with all or just the selected sequences in the alignment.
46 <br/>'Standard Databases' will check sequences against the EBI databases
47 plus any active DAS sequence sources, or you can verify against a specific
48 source from one of the sub-menus.</em><br>
50 <li><strong>Envision2 Services</strong><br/>
51 Submits one or more sequences, sequence IDs or database references to analysis workflows provided
52 by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
53 web application</a>. This allows Jalview users to easily access the EnCore network of
54 databases and analysis services developed by members of <a href="http://www.enfin.org">ENFIN</a>.
57 </strong> <em>Selecting one of the following menu items starts a remote service
58 on compute facilities at the University of Dundee. You need a continuous network
59 connection in order to use these services through Jalview. </em> </p>
61 <li><strong>Alignment</strong>
63 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
64 <em> Submits all, or just the currently selected sequences for alignment
65 with clustal W.</em></li>
66 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
67 <em> Submits the alignment or currently selected region for re-alignment
68 with clustal W. This enables you to align more sequences to an existing alignment.</em></li>
69 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
70 <em>Submits all, or just the currently selected region for alignment with
72 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
73 <em> Submits all, or just the currently selected sequences for alignment
74 using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>
77 <li><strong>Secondary Structure Prediction</strong>
79 <li><strong>JPred Secondary Structure Prediction</strong><br>
80 <em>Secondary structure prediction by network consensus. The behaviour
81 of this calculation depends on the current selection: </em></li>
82 <li><em>If nothing is selected, and the displayed sequences appear to be
83 aligned, then a JNet prediction will be run for the first sequence in
84 the alignment, using the current alignment. Otherwise the first sequence
85 will be submitted for prediction. </em></li>
86 <li><em>If just one sequence (or a region on one sequence) has been selected,
87 it will be submitted to the automatic JNet prediction server for homolog
88 detection and prediction. </em></li>
89 <li><em>If a set of sequences are selected, and they appear to be aligned,
90 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
91 sequence in the set (that is, the one that appears first in the alignment
96 <p><strong> </strong></p>