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