2 <head><title>Web Service Menu</title></head>
5 <p><strong>Web Service Menu</strong></p>
7 <li><strong>Fetch DB References</strong><br>
8 <em>This will use any of the database services that Jalview is aware
9 of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
10 to verify the sequence and retrieve all database cross references and PDB ids
11 associated with all or just the selected sequences in the alignment.
12 <br/>'Standard Databases' will check sequences against the EBI databases
13 plus any active DAS sequence sources, or you can verify against a specific
14 source from one of the sub-menus.</em><br>
16 <li><strong>Envision2 Services</strong><br/>
17 Submits one or more sequences, sequence IDs or database references to analysis workflows provided
18 by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
19 web application</a>. This allows Jalview users to easily access the EnCore network of
20 databases and analysis services developed by members of <a href="http://www.enfin.org">ENFIN</a>.
23 </strong> <em>Selecting one of the following menu items starts a remote service
24 on compute facilities at the University of Dundee. You need a continuous network
25 connection in order to use these services through Jalview. </em> </p>
27 <li><strong>Alignment</strong>
29 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
30 <em> Submits all, or just the currently selected sequences for alignment
31 with clustal W.</em></li>
32 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
33 <em> Submits the alignment or currently selected region for re-alignment
34 with clustal W. This enables you to align more sequences to an existing alignment.</em></li>
35 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
36 <em>Submits all, or just the currently selected region for alignment with
38 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
39 <em> Submits all, or just the currently selected sequences for alignment
40 using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>
43 <li><strong>Secondary Structure Prediction</strong>
45 <li><strong>JPred Secondary Structure Prediction</strong><br>
46 <em>Secondary structure prediction by network consensus. The behaviour
47 of this calculation depends on the current selection: </em></li>
48 <li><em>If nothing is selected, and the displayed sequences appear to be
49 aligned, then a JNet prediction will be run for the first sequence in
50 the alignment, using the current alignment. Otherwise the first sequence
51 will be submitted for prediction. </em></li>
52 <li><em>If just one sequence (or a region on one sequence) has been selected,
53 it will be submitted to the automatic JNet prediction server for homolog
54 detection and prediction. </em></li>
55 <li><em>If a set of sequences are selected, and they appear to be aligned,
56 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
57 sequence in the set (that is, the one that appears first in the alignment
62 <p><strong> </strong></p>