*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
+<head><title>Web Service Menu</title></head>
+
+<body>
+<p><strong>Web Service Menu</strong></p>
+<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>
+ <li><strong>Envision2 Services</strong><br/>
+ Submits one or more sequences, sequence IDs or database references to analysis workflows provided
+by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
+web application</a>. This allows Jalview users to easily access the EnCore network of
+databases and analysis services developed by members of <a href="http://www.enfin.org">ENFIN</a>.
+ </li>
+ </ul>
+ </strong> <em>Selecting one of the following menu items starts a remote service
+ on compute facilities at the University of Dundee. You need a continuous network
+ connection in order to use these services through Jalview. </em> </p>
+ <ul>
+ <li><strong>Alignment</strong>
+ <ul>
+ <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
+ <em> Submits all, or just the currently selected sequences for alignment
+ with clustal W.</em></li>
+ <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
+ <em> Submits the alignment or currently selected region for re-alignment
+ with clustal W. This enables you to align more sequences to an existing alignment.</em></li>
+ <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
+ <em>Submits all, or just the currently selected region for alignment with
+ MAFFT. </em> </li>
+ <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
+ <em> Submits all, or just the currently selected sequences for alignment
+ using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>
+ </ul>
+ </li>
+ <li><strong>Secondary Structure Prediction</strong>
+ <ul>
+ <li><strong>JPred Secondary Structure Prediction</strong><br>
+ <em>Secondary structure prediction by network consensus. The behaviour
+ of this calculation depends on the current selection: </em></li>
+ <li><em>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. </em></li>
+ <li><em>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. </em></li>
+ <li><em>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). </em> </li>
+ </ul>
+ </li>
+</ul>
+<p><strong> </strong></p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff