- <p><strong>Web Service Menu</strong><br /> <em>This menu
- is 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
- will use 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 the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment. <br />'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.</em><br></li>
- </ul>
- <p>Selecting items from the following submenus will start a
- remote service on compute facilities at the University of Dundee, or
- elsewhere. You need a continuous network connection in order to use
- these services through Jalview.
- </p>
- <ul>
- <li><strong>Alignment</strong><br /><em> Align the currently
- selected sequences or all sequences in the alignment, or re-align
- unaligned sequences to the aligned sequences. Entries in this menu
- provide access to the various alignment programs supported by <a
- href="../webServices/JABAWS.html">JABAWS</a>. See the <a
- href="../webServices/msaclient.html">Multiple Sequence
- Alignment webservice client</a> entry for more information.</em></li>
- <li><strong>Secondary Structure Prediction</strong>
- <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 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 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 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> sequence in the set
- (that is, the one that appears first in the alignment window).
- </li>
- </ul> </em>
- </ul></li>
- <li><strong>Analysis</strong><br />
- <ul>
- <li><strong>Multi-Harmony</strong><br> <em>Performs
- functional residue analysis on a protein family alignment with
- sub-families defined on it. See the <a
- href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
- information.</em>
- </li>
- </ul></li>
- </ul>
+ <p>
+ <strong>Web Service Menu</strong><br /> <em>This menu is
+ 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>'Retrieve full Sequence' - when checked, Jalview will
+ retrieve the full sequence for any accessions associated
+ with sequences in the alignment. <br> <strong>Note:
+ This could cause out of memory errors when working with
+ genomic sequence records !</strong><br> <strong>Added
+ in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the
+ EBI databases plus any active DAS sequence sources<</li>
+ </ul> Other submenus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em></li>
+ </ul>
+ <p>Selecting items from the following submenus will start a remote
+ service on compute facilities at the University of Dundee, or
+ elsewhere. You need a continuous network connection in order to use
+ these services through Jalview.</p>
+ <ul>
+ <li><strong>Alignment</strong><br /> <em> Align the
+ currently selected sequences or all sequences in the alignment,
+ or re-align unaligned sequences to the aligned sequences.
+ Entries in this menu provide access to the various alignment
+ programs supported by <a href="../webServices/JABAWS.html">JABAWS</a>.
+ See the <a href="../webServices/msaclient.html">Multiple
+ Sequence Alignment webservice client</a> entry for more
+ information.
+ </em></li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <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
+ 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
+ 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
+ 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>
+ sequence in the set (that is, the one that appears first
+ in the alignment window).
+ </li>
+ </ul>
+ </em>
+ </ul></li>
+ <li><strong>Analysis</strong><br />
+ <ul>
+ <li><strong>Multi-Harmony</strong><br> <em>Performs
+ functional residue analysis on a protein family alignment
+ with sub-families defined on it. See the <a
+ href="../webServices/shmr.html">Multi-Harmony
+ service</a> entry for more information.
+ </em></li>
+ </ul></li>
+ </ul>