--- /dev/null
+<html>\r
+<head><title>ClustalW Alignment</title></head>\r
+<body>\r
+<p><strong>ClustalW Alignments</strong></p>\r
+<p>ClustalW is a program for multiple sequence alignment. It works\r
+with both DNA and protein sequences, and can also perform profile\r
+profile alignments to align two or more multiple sequence\r
+alignments.</p>\r
+<p>\r
+Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) <br>\r
+CLUSTAL W: improving the sensitivity of progressive multiple\r
+sequence alignment through sequence weighting, position specific gap\r
+penalties and weight matrix choice.<br>\r
+<em>Nucleic Acids Research</em> <strong>22</strong> 4673-4680\r
+</p>\r
+<p>There are two versions of this alignment function, which will operate\r
+on the selected region, if any, or the whole sequence set:</p>\r
+<ul>\r
+<li><strong>Calculations→Web Service→Clustal\r
+Alignment..</strong><br>\r
+Aligns using the clustalW program, ignoring any gaps in the submitted\r
+sequence set.\r
+</li>\r
+<li><strong>Calculations→Web Service→Clustal\r
+Realign..</strong><br>\r
+Submits the sequences with existing gaps to clustalW, which will\r
+preserve existing gaps and re-align those regions which are not optimal.\r
+</li>\r
+</ul>\r
+</body>\r
+</html>\r
--- /dev/null
+<html>
+<head>
+<title>JNet Secondary Structure Prediction</title>
+</head>
+<body>
+<strong>JNet Secondary Structure Prediction</strong>
+<p>
+Secondary structure prediction methods attempts to infer the likely secondary
+structure for a protein based on its amino acid composition and
+similarity to sequences with known secondary structure. The JNet
+method uses several different prediction methods and decides on the
+most likely prediction via a jury network. <br>
+<ul>
+<li>Cuff J. A and Barton G.J (1999) Application of enhanced multiple
+sequence alignment profiles to improve protein secondary
+structure prediction <em>Proteins</em> <strong>40</strong> 502-511</li></ul>
+</p>
+The function available from the <strong>Calculations→Web
+Service→JNet...</strong> menu does two different kinds of
+prediction, dependent upon the currently selected region:</p>
+<ul>
+<li>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.
+</li>
+<li>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.
+</li>
+<li>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 selected in the set (that is, the one
+that was first clicked on).
+</li>
+</ul>
+<p>The result of a JNet prediction for a sequence is a new annotated
+ alignment window:</p>
+<img src="jnetprediction.gif">
+<p>
+The sequence for which the prediction was made is the first one in the
+alignment. If a sequence based prediction was made then the remaining
+sequences in the alignment are the aligned parts of homologs which
+were used to construct a sequence profile for the prediction. If the
+prediction was made using a multiple alignment, then the original
+multiple alignment will be returned, annotated with the prediction.
+</p>
+The annotation bars below the alignment are as follows:</p>
+<ul>
+<li>Lupas_21, Lupas_14, Lupas_28<br>
+<em>Coiled-coil predictions for the sequence. These are binary
+predictions for each location.</em></li>
+<li>JNETSOL25,JNETSOL5,JNETSOL0<br>
+<em>Solvent accessibility predictions - binary predictions of 25%, 5%
+or 0% solvent accessibility.</em></li>
+<li>JNetPRED<br>
+<em>The consensus prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>JNetCONF<br>
+<em>The confidence estimate for the prediction. High values mean high
+confidence. prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>JNetALIGN<br>
+<em>Alignment based prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>JNetHMM<br>
+<em>HMM profile based prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>jpred<br>
+<em>Jpred prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>JNETPSSM<br>
+<em>PSSM based prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>JNETFREQ<br>
+<em>Amino Acid frequency based prediction - helices are marked as red tubes, and
+sheets as dark green arrows.</em></li>
+<li>JNETJURY<br>
+<em>A '*' in this annotation indicates that the JNETJURY was invoked
+to rationalise significantly different primary predictions.</em></li>
+</ul>
+</p>
+</body>
+</html>
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