Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950

[jalview.git] / help / html / menus / wsmenu.html

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 33282e9..b8b357e 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -29,14 +29,13 @@
       dynamic, and may contain user-defined web service entries in
       addition to any of the following ones:</em>
   <ul>
-    <li><strong>Fetch DB References</strong><br> <em>This
-        submenu contains options for accessing any of the database
-        services that Jalview is aware of (e.g. DAS sequence servers and
-        the WSDBFetch service provided by the EBI) to verify sequence
-        start/end positions and retrieve all database cross references
-        and PDB ids associated with all or just the selected sequences
-        in the alignment.
-        <ul>
+    <li><strong>Fetch DB References</strong><br> <em>This submenu
+                               contains options for accessing any of the database services that
+                               Jalview is aware of (e.g services provided by the EBI) to verify
+                               sequence start/end positions and retrieve all database cross
+                               references and PDB ids associated with all or just the selected
+                               sequences in the alignment.
+                               <ul>
           <li>'Retrieve full Sequence' - when checked, Jalview will
             retrieve the full sequence for any accessions associated
             with sequences in the alignment. <br> <strong>Note:
@@ -45,7 +44,7 @@
               in Jalview 2.8.1</strong>
           </li>
           <li>'Standard Databases' will check sequences against the
-            EBI databases plus any active DAS sequence sources<</li>
+            EBI databases</li>
         </ul> Other submenus allow you to pick a specific source to query -
         sources are listed alphabetically according to their nickname.
     </em></li>
@@ -68,22 +67,22 @@
       <ul>
         <li><strong>JPred Secondary Structure Prediction</strong><br>
           <em>Secondary structure prediction by network consensus.
-            See the <a href="../webServices/jnet.html">Jpred3</a> client
+            See the <a href="../webServices/jnet.html">Jpred</a> client
             entry for more information. The behaviour of this
             calculation depends on the current selection:
             <ul>
               <li>If nothing is selected, and the displayed
-                sequences appear to be aligned, then a JNet prediction
+                sequences appear to be aligned, then a JPred prediction
                 will be run for the first sequence in the alignment,
                 using the current alignment. Otherwise the first
                 sequence will be submitted for prediction.</li>
               <li>If just one sequence (or a region on one
                 sequence) has been selected, it will be submitted to the
-                automatic JNet prediction server for homolog detection
+                automatic JPred prediction server for homolog detection
                 and prediction.</li>
               <li>If a set of sequences are selected, and they
                 appear to be aligned, then the alignment will be used
-                for a Jnet prediction on the <strong>first</strong>
+                for a JPred prediction on the <strong>first</strong>
                 sequence in the set (that is, the one that appears first
                 in the alignment window).
               </li>