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.</em><br>
14 </strong> <em>Selecting one of the following menu items starts a remote service
15 on compute facilities at the University of Dundee. You need a continuous network
16 connection in order to use these services through Jalview. </em> </p>
18 <li><strong>Alignment</strong>
20 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
21 <em> Submits all, or just the currently selected sequences for alignment
22 with clustal W.</em></li>
23 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
24 <em> Submits the alignment or currently selected region for re-alignment
25 with clustal W. Use this if you have added some new sequences to an existing
27 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
28 <em>Submits all, or just the currently selected region for alignment with
30 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
31 <em> Submits all, or just the currently selected sequences for alignment
32 using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>
35 <li><strong>Secondary Structure Prediction</strong>
37 <li><strong>JPred Secondary Structure Prediction</strong><br>
38 <em>Secondary structure prediction by network consensus. The behaviour
39 of this calculation depends on the current selection: </em></li>
40 <li><em>If nothing is selected, and the displayed sequences appear to be
41 aligned, then a JNet prediction will be run for the first sequence in
42 the alignment, using the current alignment. Otherwise the first sequence
43 will be submitted for prediction. </em></li>
44 <li><em>If just one sequence (or a region on one sequence) has been selected,
45 it will be submitted to the automatic JNet prediction server for homolog
46 detection and prediction. </em></li>
47 <li><em>If a set of sequences are selected, and they appear to be aligned,
48 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
49 sequence in the set (that is, the one that appears first in the alignment
54 <p><strong> </strong></p>