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:
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>
<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>