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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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* This file is part of Jalview.
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<title>AACon Web Service</title>
</head>
<body>
- <strong>AACon Alignment Conservation Calculation Service</strong>
- <p>The JABAWS AACon service implements 17 different conservation
- scores for protein sequence alignments.</p>
- <p>
- The majority of these scores were described by Valdar in 2002 (Scoring
- residue conservation. <em>Proteins: Structure, Function, and
- Genetics</em> 43(2): 227-241. <a
- href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a> or
- available on the <a
- href="http://www.well.ox.ac.uk/~valdar/publications.html">Valdar
- Group publications page</a>), but the SMERFs score was developed later
- and described by Manning et al. in 2008 (<a
- href="http://www.biomedcentral.com/1471-2105/9/51">BMC
- Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
- </p>
- <p>
- <strong>Enabling and disabling AACon calculations</strong><br /> When
- the <strong>AACon Calculation</strong> entry in the <strong>Web
- Services→Conservation</strong> is ticked, AACon calculations will be
- performed every time the alignment is modified. Selecting the menu
- item will enable or disable automatic recalculation.
- </p>
- <p>
- <strong>Configuring which AACon calculations are performed</strong><br />
- The <strong>Web Services→Conservation→Change AACon
- Settings ...</strong> menu entry will open a <a href="webServicesParams.html">web
- services parameter dialog</a> for the currently configured AACon server.
- Standard presets are provided for quick and more expensive
- conservation calculations, and parameters are also provided to change
- the way that SMERFS calculations are performed.<br /> <em>AACon
- settings for an alignment are saved in <a
- href="../features/jalarchive.html">Jalview projects</a> along with
- the latest calculation results.
- </em>
- </p>
- <p>
- <strong>Changing the server used for AACon calculations</strong><br />
- If you are working with alignments too large to analyse with the
- public JABAWS server, then you will most likely have already
- configured <a href="webServicesPrefs.html">additional JABAWS
- servers</a>. By default, Jalview will chose the first AACon service
- available from the list of JABAWS servers available. If available, you can switch to
- use another AACon service by selecting it from the <strong>Web
- Services→Conservation→Switch Server</strong> submenu.
- </p>
+ <strong>AACon Alignment Conservation Calculation Service</strong>
+ <p>The JABAWS AACon service implements 17 different conservation
+ scores for protein sequence alignments.</p>
+ <p>
+ The majority of these scores were described by Valdar in 2002
+ (Scoring residue conservation. <em>Proteins: Structure,
+ Function, and Genetics</em> 43(2): 227-241. <a
+ href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a>
+ or available on the <a
+ href="http://valdarlab.unc.edu/publications.html">Valdar
+ Group publications page</a>), but the SMERFs score was developed later
+ and described by Manning et al. in 2008 (<a
+ href="http://www.biomedcentral.com/1471-2105/9/51">BMC
+ Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
+ </p>
+ <p>
+ <strong>Enabling and disabling AACon calculations</strong><br />
+ When the <strong>AACon Calculation</strong> entry in the <strong>Web
+ Services→Conservation</strong> is ticked, AACon calculations will be
+ performed every time the alignment is modified. Selecting the menu
+ item will enable or disable automatic recalculation.
+ </p>
+ <p>
+ <strong>Configuring which AACon calculations are performed</strong><br />
+ The <strong>Web Services→Conservation→Change
+ AACon Settings ...</strong> menu entry will open a <a
+ href="webServicesParams.html">web services parameter
+ dialog</a> for the currently configured AACon server. Standard presets
+ are provided for quick and more expensive conservation calculations,
+ and parameters are also provided to change the way that SMERFS
+ calculations are performed.<br /> <em>AACon settings for an
+ alignment are saved in <a href="../features/jalarchive.html">Jalview
+ projects</a> along with the latest calculation results.
+ </em>
+ </p>
+ <p>
+ <strong>Changing the server used for AACon calculations</strong><br />
+ If you are working with alignments too large to analyse with the
+ public JABAWS server, then you will most likely have already
+ configured <a href="webServicesPrefs.html">additional JABAWS
+ servers</a>. By default, Jalview will chose the first AACon service
+ available from the list of JABAWS servers available. If available,
+ you can switch to use another AACon service by selecting it from the
+ <strong>Web Services→Conservation→Switch Server</strong>
+ submenu.
+ </p>
</body>
</html>
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