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