X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwebServices%2FproteinDisorder.html;h=1c35bf3ca3c252916581e668906d02e79a1d90e4;hb=refs%2Fheads%2Ffeatures%2FJAL-2040_JAL-2137_phyre2;hp=53c08222485045203713efeb6a2ee213cf1209b9;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html
index 53c0822..1c35bf3 100644
--- a/help/html/webServices/proteinDisorder.html
+++ b/help/html/webServices/proteinDisorder.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -28,26 +28,25 @@
     The <strong>Web Services&rarr;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 or currently selected region (<em>since Jalview
-      2.8.0b1</em>) to identify regions likely to be unstructured or
-    flexible, or alternately, fold to form globular domains.
+      href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS
+      servers</a>. Each service operates on sequences in the alignment or
+    currently selected region (<em>since Jalview 2.8.0b1</em>) 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>
+      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.
+      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>
@@ -74,10 +73,10 @@
       <td>Sequence Feature &amp;<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.
+        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>
@@ -117,13 +116,13 @@
 
   <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.
+      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>
@@ -147,14 +146,13 @@
   </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.
+      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>
@@ -196,17 +194,16 @@
   </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 />
+      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>
