3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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21 <title>AACon Web Service</title>
24 <strong>AACon Alignment Conservation Calculation Service</strong>
25 <p>The JABAWS AACon service implements 17 different conservation
26 scores for protein sequence alignments.</p>
28 The majority of these scores were described by Valdar in 2002 (Scoring
29 residue conservation. <em>Proteins: Structure, Function, and
30 Genetics</em> 43(2): 227-241. <a
31 href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a> or
33 href="http://www.well.ox.ac.uk/~valdar/publications.html">Valdar
34 Group publications page</a>), but the SMERFs score was developed later
35 and described by Manning et al. in 2008 (<a
36 href="http://www.biomedcentral.com/1471-2105/9/51">BMC
37 Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
40 <strong>Enabling and disabling AACon calculations</strong><br /> When
41 the <strong>AACon Calculation</strong> entry in the <strong>Web
42 Services→Conservation</strong> is ticked, AACon calculations will be
43 performed every time the alignment is modified. Selecting the menu
44 item will enable or disable automatic recalculation.
47 <strong>Configuring which AACon calculations are performed</strong><br />
48 The <strong>Web Services→Conservation→Change AACon
49 Settings ...</strong> menu entry will open a <a href="webServicesParams.html">web
50 services parameter dialog</a> for the currently configured AACon server.
51 Standard presets are provided for quick and more expensive
52 conservation calculations, and parameters are also provided to change
53 the way that SMERFS calculations are performed.<br /> <em>AACon
54 settings for an alignment are saved in <a
55 href="../features/jalarchive.html">Jalview projects</a> along with
56 the latest calculation results.
60 <strong>Changing the server used for AACon calculations</strong><br />
61 If you are working with alignments too large to analyse with the
62 public JABAWS server, then you will most likely have already
63 configured <a href="webServicesPrefs.html">additional JABAWS
64 servers</a>. By default, Jalview will chose the first AACon service
65 available from the list of JABAWS servers available. If available, you can switch to
66 use another AACon service by selecting it from the <strong>Web
67 Services→Conservation→Switch Server</strong> submenu.