3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
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15 * PURPOSE. See the GNU General Public License for more details.
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20 <title>AACon Web Service</title>
23 <strong>AACon Alignment Conservation Calculation Service</strong>
24 <p>The JABAWS AACon service implements 17 different conservation
25 scores for protein sequence alignments.</p>
27 The majority of these scores were described by Valdar in 2002 (Scoring
28 residue conservation. <em>Proteins: Structure, Function, and
29 Genetics</em> 43(2): 227-241. <a
30 href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a> or
32 href="http://www.well.ox.ac.uk/~valdar/publications.html">Valdar
33 Group publications page</a>), but the SMERFs score was developed later
34 and described by Manning et al. in 2008 (<a
35 href="http://www.biomedcentral.com/1471-2105/9/51">BMC
36 Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
39 <strong>Enabling and disabling AACon calculations</strong><br /> When
40 the <strong>AACon Calculation</strong> entry in the <strong>Web
41 Services→Conservation</strong> is ticked, AACon calculations will be
42 performed every time the alignment is modified. Selecting the menu
43 item will enable or disable automatic recalculation.
46 <strong>Configuring which AACon calculations are performed</strong><br />
47 The <strong>Web Services→Conservation→Change AACon
48 Settings ...</strong> menu entry will open a <a href="webServicesParams.html">web
49 services parameter dialog</a> for the currently configured AACon server.
50 Standard presets are provided for quick and more expensive
51 conservation calculations, and parameters are also provided to change
52 the way that SMERFS calculations are performed.<br /> <em>AACon
53 settings for an alignment are saved in <a
54 href="../features/jalarchive.html">Jalview projects</a> along with
55 the latest calculation results.
59 <strong>Changing the server used for AACon calculations</strong><br />
60 If you are working with alignments too large to analyse with the
61 public JABAWS server, then you will most likely have already
62 configured <a href="webServicesPrefs.html">additional JABAWS
63 servers</a>. By default, Jalview will chose the first AACon service
64 available from the list of JABAWS servers available. If available, you can switch to
65 use another AACon service by selecting it from the <strong>Web
66 Services→Conservation→Switch Server</strong> submenu.