<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 retrieving sequence cross-references such as the
- protein products of a DNA sequence.
+ 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>
<p>
<strong>Initiating reference retrieval</strong><br> The
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
<p>
<strong>The Sequence Identification Process</strong><br> The
method of accession id discovery is derived from the method which
- earlier Jalview versions used for Uniprot sequence feature retrieval,
- and was originally restricted to the identification of valid Uniprot
+ earlier Jalview versions used for UniProt sequence feature retrieval,
+ and was originally restricted to the identification of valid UniProt
accessions.<br> Essentially, Jalview will try to retrieve records
from a subset of the databases accessible by the <a
- href="../features/seqfetch.html"
- >sequence fetcher</a> using each sequence's ID string (or each string in
- the ID separated by the '∣' symbol).
+ href="../features/seqfetch.html">sequence fetcher</a> using each
+ sequence's ID string (or each string in the ID separated by the
+ '∣' symbol).
</p>
<p>If a record (or set of records) is retrieved by any query derived
from the ID string of a sequence, then the sequence is aligned to the