<!--
- * 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.
*
<p>
<p>
<strong>Discovering Database References for Sequences</strong><br>
- Database references are associated with a sequence are displayed as a
- list in the tooltip shown when mousing over its sequence ID. Jalview
- uses references for the retrieval of <a
- href="../features/viewingpdbs.html">PDB structures</a> and <a
- href="../features/dasfeatures.html">DAS features</a>, and for
+ Database references associated with a sequence are displayed as an
+ abbreviated list in the tooltip shown when mousing over its sequence
+ ID, and can be viewed in full via the
+ <a href="../io/exportseqreport.html">Sequence Details</a> window. .
+ Jalview also uses references for the retrieval of
+ <a href="../features/viewingpdbs.html">PDB structures</a>, and for
retrieving sequence cross-references such as the protein products of a
DNA sequence.
</p>
application provides three ways to access the retrieval function.
Either:
<ul>
- <li>select the <strong>Discover PDB IDs</strong> option from the
- structure submenu of the sequence's popup menu
- </li>
- <li>Choose one of the options from the 'Fetch DB Refs' submenu in
+ <li>select the <strong>Structure Chooser...</strong> option from
+ the Sequence ID popup menu.
+ </li>
+ <li>Choose one of the options from the 'Fetch DB Refs' submenu in
the alignment window's <strong>Web Services</strong> menu:
<ul>
- <li><em>Standard Databases</em> will fetch references from
- the EBI databases plus currently selected DAS sources</li>
- <li>The other entries submenus leading to lists of individual
+ <li><em>Standard Databases</em> will fetch references from EBI
+ databases appropriate for the sequence type (Nucleotide or Protein)</li>
+ <li>The other entries submenus leading to lists of individual
database sources that Jalview can access.</li>
</ul>
</li>
- <li>Answer 'Yes' when asked if you wish to retrieve database
- references for your sequences after initiating a DAS Sequence
- Feature fetch.</li>
</ul>
<p>Jalview discovers references for a sequence by generating a set
of ID queries from the ID string of each sequence in the alignment. It