2 <head><title>Web Service Menu</title></head>
5 <p><strong>Web Service Menu</strong></p>
7 </strong> <em>Selecting one of the following menu items starts a remote service
8 on compute facilities at the University of Dundee. You need a continuous network
9 connection in order to use these services through Jalview. </em> </p>
11 <li><strong>Fetch DB References</strong><br>
12 <em>This will use the service WSDBFetch, provided by the EBI, to retrieve all
13 uniprot database cross references and PDB ids associated with the selected sequences in
14 the alignment if the sequences have valid Uniprot names or accession ids.</em><br>
16 <li><strong>Alignment</strong>
18 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
19 <em> Submits all, or just the currently selected sequences for alignment
20 with clustal W.</em></li>
21 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
22 <em> Submits the alignment or currently selected region for re-alignment
23 with clustal W. Use this if you have added some new sequences to an existing
25 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
26 <em>Submits all, or just the currently selected region for alignment with
28 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
29 <em> Submits all, or just the currently selected sequences for alignment
30 using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>
33 <li><strong>Secondary Structure Prediction</strong>
35 <li><strong>JPred Secondary Structure Prediction</strong><br>
36 <em>Secondary structure prediction by network consensus. The behaviour
37 of this calculation depends on the current selection: </em></li>
38 <li><em>If nothing is selected, and the displayed sequences appear to be
39 aligned, then a JNet prediction will be run for the first sequence in
40 the alignment, using the current alignment. Otherwise the first sequence
41 will be submitted for prediction. </em></li>
42 <li><em>If just one sequence (or a region on one sequence) has been selected,
43 it will be submitted to the automatic JNet prediction server for homolog
44 detection and prediction. </em></li>
45 <li><em>If a set of sequences are selected, and they appear to be aligned,
46 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
47 sequence in the set (that is, the one that appears first in the alignment
52 <p><strong> </strong></p>