--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<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>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>JABAWS Protein Disorder Prediction Services</title>
+</head>
+<body>
+ <p>
+ <strong>JABAWS Protein Disorder Prediction Services</strong> <br />
+ The <strong>Web Services→Disorder</strong> menu in the alignment
+ window allows access to protein disorder prediction services provided
+ by the configured <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
+ servers</a>. Each service operates on sequences in the alignment to
+ identify regions likely to be unstructured or flexible, or
+ alternately, fold to form globular domains.
+ </p>
+ <p>
+ Predictor results include both <a href="../features/seqfeatures.html">sequence
+ features</a> and sequence associated <a
+ href="../features/annotation.html">alignment annotation</a> rows.
+ Features display is controlled from the <a
+ href="../features/featureSettings.html">Feature Settings</a> dialog
+ box. Clicking on the ID for a disorder prediction annotation row will
+ highlight or select (if double clicked) the associated sequence for
+ that row. You can also use the <em>Sequence Associated</em> option in
+ the <a href="../colourSchemes/annotationColouring.html">Colour By
+ Annotation</a> dialog box to colour sequences according to the results of
+ predictors shown as annotation rows.
+ </p>
+ <p>JABAWS 2.0 provides four disorder predictors which are described
+ below:</p>
+ <ul>
+ <li><a href="#disembl">DisEMBL</a></li>
+ <li><a href="#iupred">IUPred</a></li>
+ <li><a href="#ronn">RONN</a></li>
+ <li><a href="#globplot">GlobPlot</a></li>
+ </ul>
+ <p>
+ <strong><a name="disembl"></a><a href="http://dis.embl.de/">DisEMBL
+ (Linding et al., 2003)</a> </strong> <br /> DisEMBL is a set of machine-learning
+ based predictors trained to recognise disorder-related annotation
+ found on PDB structures.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>COILS</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>Predicts loops/coils according to DSSP definition<a
+ href="#dsspstates">[1]</a>.<br />Features mark range(s) of residues
+ predicted as loops/coils, and annotation row gives raw value for
+ each residue. Value over 0.516 indicates loop/coil.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>HOTLOOPS</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>"Hot loops constitute a refined subset of <strong>COILS</strong>,
+ namely those loops with a high degree of mobility as determined from
+ Cα temperature factors (B factors). It follows that highly
+ dynamic loops should be considered protein disorder."<br />
+ Features mark range(s) of residues predicted to be hot loops and
+ annotation row gives raw value for each residue. Values over 0.6
+ indicates hot loop.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>REMARK465</strong></td>
+ <td>Sequence Feature &<br />Annotation Row
+ </td>
+ <td>"Missing coordinates in X-ray structure as defined by
+ remark465 entries in PDB. Nonassigned electron densities most often
+ reflect intrinsic disorder, and have been used early on in disorder
+ prediction."<br /> Features gives range(s) of residues
+ predicted as disordered, and annotation row gives raw value for each
+ residue. Value over 0.1204 indicates disorder.
+ </td>
+ </tr>
+ </table>
+
+ <p>
+ <a name="dsspstates"></a>[1]. DSSP Classification: α-helix (H),
+ 310-helix (G), β-strand (E) are ordered, and all other states
+ (β-bridge (B), β-turn (T), bend (S), π-helix (I), and
+ coil (C)) considered loops or coils.
+ </p>
+
+
+ <p>
+ <strong><a name="ronn"></a><a
+ href="http://www.strubi.ox.ac.uk/RONN">RONN</a></strong> <em>a.k.a.</em>
+ Regional Order Neural Network<br />This predictor employs an approach
+ known as the 'bio-basis' method to predict regions of disorder in
+ sequences based on their local similarity with a gold-standard set of
+ disordered protein sequences. It yields a set of disorder prediction
+ scores, which are shown as sequence annotation below the alignment.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>JRonn</strong>[2]</td>
+ <td>Annotation Row</td>
+ <td>RONN score for each residue in the sequence. Scores above
+ 0.5 identify regions of the protein likely to be disordered.</td>
+ </tr>
+ </table>
+ <p>
+ <em>[2]. JRonn denotes the score for this server because JABAWS
+ runs a Java port of RONN developed by Peter Troshin and distributed
+ as part of <a href="http://www.biojava.org/">Biojava 3</a>
+ </em>
+ </p>
+ <p>
+ <strong><a name="iupred"></a><a
+ href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br /> IUPred
+ employs an empirical model to estimate likely regions of disorder.
+ There are three different prediction types offered, each using
+ different parameters optimized for slightly different applications. It
+ provides raw scores based on two models for predicting regions of
+ 'long disorder' and 'short disorder'. A third predictor identifies
+ regions likely to form structured domains.
+ </p>
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>Long disorder</strong></td>
+ <td>Annotation Row</td>
+ <td>Prediction of context-independent global disorder that
+ encompasses at least 30 consecutive residues of predicted disorder.
+ Employs a 100 residue window for calculation.<br />Values above 0.5
+ indicates the residue is intrinsically disordered.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Short disorder</strong></td>
+ <td>Annotation Row</td>
+ <td>Predictor for short, (and probably) context-dependent,
+ disordered regions, such as missing residues in the X-ray structure
+ of an otherwise globular protein. Employs a 25 residue window for
+ calculation, and includes adjustment parameter for chain termini
+ which favors disorder prediction at the ends.<br />Values above 0.5
+ indicate short-range disorder.
+ </td>
+ </tr>
+ <tr>
+ <td><strong>Structured domains</strong></td>
+ <td>Sequence Feature</td>
+ <td>Features highlighting likely globular domains useful for
+ structure genomics investigation. <br />Post-analysis of disordered
+ region profile to find continuous regions confidently predicted to
+ be ordered. Neighbouring regions close to each other are merged,
+ while regions shorter than the minimal domain size of at least 30
+ residues are ignored.
+ </td>
+ </tr>
+ </table>
+ <p>
+ <strong><a name="globplot"></a><a
+ href="http://globplot.embl.de/">GLOBPLOT</a></strong><br /> Defines regions
+ of globularity or natively unstructured regions based on a running sum
+ of the propensity of residues to be structured or unstructured. The
+ propensity is calculated based on the probability of each amino acid
+ being observed within well defined regions of secondary structure or
+ within regions of random coil. The initial signal is smoothed with a
+ Savitzky-Golay filter, and its first order derivative computed.
+ Residues for which the first order derivative is positive are
+ designated as natively unstructured, whereas those with negative
+ values are structured.<br />
+ <table border="1">
+ <tr>
+ <td><strong>Name</strong></td>
+ <td><strong>Annotation type</strong></td>
+ <td><strong>Description</strong></td>
+ </tr>
+ <tr>
+ <td><strong>Disordered Region</strong></td>
+ <td>Sequence Feature</td>
+ <td><br />Sequence features marking range(s) of residues with
+ positive dydx values (correspond to the #Disorder column from JABAWS
+ results)</td>
+ </tr>
+ <tr>
+ <td><strong>Globular Domain</strong>
+ <td>Sequence Feature</td>
+ <td>Putative globular domains</td>
+ </tr>
+ <tr>
+ <td><strong>Dydx</strong></td>
+ <td>Annotation row</td>
+ <td>First order derivative of smoothed score. Values above 0
+ indicates residue is disordered.</td>
+ </tr>
+ <tr>
+ <td><strong>Smoothed Score<br />Raw Score
+ </strong></td>
+ <td>Annotation Row</td>
+ <td>The smoothed and raw scores used to create the differential
+ signal that indicates the presence of unstructured regions.<br /> <em>These
+ are hidden by default, but can be shown by right-clicking on the
+ alignment annotation panel and selecting <strong>Show
+ hidden annotation</strong>
+ </em>
+ </td>
+ </tr>
+ </table>
+ <p>
+ <em>Documentation and thresholds for the JABAWS Disorder
+ predictors adapted from a personal communication by Nancy Giang,
+ 2012.</em>
+ </p>
+</body>
+</html>
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