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.
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9 * modify it under the terms of the GNU General Public License
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11 * of the License, or (at your option) any later version.
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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.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Web Service Menu</title>
28 <strong>Web Service Menu</strong><br /> <em>This menu is
29 dynamic, and may contain user-defined web service entries in
30 addition to any of the following ones:</em>
32 <li><strong>Fetch DB References</strong><br> <em>This
33 submenu contains options for accessing any of the database
34 services that Jalview is aware of (e.g. DAS sequence servers and
35 the WSDBFetch service provided by the EBI) to verify sequence
36 start/end positions and retrieve all database cross references
37 and PDB ids associated with all or just the selected sequences
40 <li>'Retrieve full Sequence' - when checked, Jalview will
41 retrieve the full sequence for any accessions associated
42 with sequences in the alignment. <br> <strong>Note:
43 This could cause out of memory errors when working with
44 genomic sequence records !</strong><br> <strong>Added
45 in Jalview 2.8.1</strong>
47 <li>'Standard Databases' will check sequences against the
48 EBI databases plus any active DAS sequence sources<</li>
49 </ul> Other submenus allow you to pick a specific source to query -
50 sources are listed alphabetically according to their nickname.
53 <p>Selecting items from the following submenus will start a remote
54 service on compute facilities at the University of Dundee, or
55 elsewhere. You need a continuous network connection in order to use
56 these services through Jalview.</p>
58 <li><strong>Alignment</strong><br /> <em> Align the
59 currently selected sequences or all sequences in the alignment,
60 or re-align unaligned sequences to the aligned sequences.
61 Entries in this menu provide access to the various alignment
62 programs supported by <a href="../webServices/JABAWS.html">JABAWS</a>.
63 See the <a href="../webServices/msaclient.html">Multiple
64 Sequence Alignment webservice client</a> entry for more
67 <li><strong>Secondary Structure Prediction</strong>
69 <li><strong>JPred Secondary Structure Prediction</strong><br>
70 <em>Secondary structure prediction by network consensus.
71 See the <a href="../webServices/jnet.html">Jpred3</a> client
72 entry for more information. The behaviour of this
73 calculation depends on the current selection:
75 <li>If nothing is selected, and the displayed
76 sequences appear to be aligned, then a JNet prediction
77 will be run for the first sequence in the alignment,
78 using the current alignment. Otherwise the first
79 sequence will be submitted for prediction.</li>
80 <li>If just one sequence (or a region on one
81 sequence) has been selected, it will be submitted to the
82 automatic JNet prediction server for homolog detection
84 <li>If a set of sequences are selected, and they
85 appear to be aligned, then the alignment will be used
86 for a Jnet prediction on the <strong>first</strong>
87 sequence in the set (that is, the one that appears first
88 in the alignment window).
93 <li><strong>Analysis</strong><br />
95 <li><strong>Multi-Harmony</strong><br> <em>Performs
96 functional residue analysis on a protein family alignment
97 with sub-families defined on it. See the <a
98 href="../webServices/shmr.html">Multi-Harmony
99 service</a> entry for more information.