-<html>\r
-<head><title>Web Service Menu</title></head>\r
-\r
-<body>\r
-<p><strong>Web Service Menu</strong></p>\r
-<p><strong><br>\r
- </strong> <em>Selecting one of the following menu items starts a remote service \r
- on compute facilities at the University of Dundee. You need a continuous network \r
- connection in order to use these services through Jalview. </em> </p>\r
-<ul>\r
- <li><strong>Fetch DB References</strong><br>\r
- This will use the service WSDBFetch, provided by the EBI, to retrieve all \r
- database references and PDB ids associated with the selected sequences in \r
- the alignment if the sequences have valid Uniprot names or accession ids. \r
- </li>\r
- <li><strong>Alignment</strong> \r
- <ul>\r
- <li><strong>ClustalW Multiple Sequence Alignment</strong><br>\r
- <em> Submits all, or just the currently selected sequences for alignment \r
- with clustal W.</em></li>\r
- <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>\r
- <em> Submits the alignment or currently selected region for re-alignment \r
- with clustal W. Use this if you have added some new sequences to an existing \r
- alignment.</em></li>\r
- <li><strong>MAFFT Multiple Sequence Alignment</strong><br>\r
- <em>Submits all, or just the currently selected region for alignment with \r
- MAFFT. </em> </li>\r
- <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
- <em> Submits all, or just the currently selected sequences for alignment \r
- using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>\r
- </ul>\r
- </li>\r
- <li><strong>Secondary Structure Prediction</strong> \r
- <ul>\r
- <li><strong>JPred Secondary Structure Prediction</strong><br>\r
- <em>Secondary structure prediction by network consensus. The behaviour \r
- of this calculation depends on the current selection: </em></li>\r
- <li><em>If nothing is selected, and the displayed sequences appear to be \r
- aligned, then a JNet prediction will be run for the first sequence in \r
- the alignment, using the current alignment. Otherwise the first sequence \r
- will be submitted for prediction. </em></li>\r
- <li><em>If just one sequence (or a region on one sequence) has been selected, \r
- it will be submitted to the automatic JNet prediction server for homolog \r
- detection and prediction. </em></li>\r
- <li><em>If a set of sequences are selected, and they appear to be aligned, \r
- then the alignment will be used for a Jnet prediction on the <strong>first</strong> \r
- sequence in the set (that is, the one that appears first in the alignment \r
- window). </em> </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-<p><strong> </strong></p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Web Service Menu</title></head>
+
+<body>
+<p><strong>Web Service Menu</strong></p>
+<p><strong><br>
+ </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>Fetch DB References</strong><br>
+ <em>This will use the service WSDBFetch, provided by the EBI, to retrieve all
+ uniprot database cross references and PDB ids associated with the selected sequences in
+ the alignment if the sequences have valid Uniprot names or accession ids.</em><br>
+ </li>
+ <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. Use this if you have added some new 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 / commitdiff