-<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>
+<html>\r
+<head>\r
+<title>JNet Secondary Structure Prediction</title>\r
+</head>\r
+<body>\r
+<strong>JNet Secondary Structure Prediction</strong>\r
+<p>\r
+Secondary structure prediction methods attempts to infer the likely secondary\r
+structure for a protein based on its amino acid composition and\r
+similarity to sequences with known secondary structure. The JNet\r
+method uses several different prediction methods and decides on the\r
+most likely prediction via a jury network. <br>\r
+<ul>\r
+<li>Cuff J. A and Barton G.J (1999) Application of enhanced multiple\r
+sequence alignment profiles to improve protein secondary\r
+structure prediction <em>Proteins</em> <strong>40</strong> 502-511</li></ul>\r
+</p>\r
+The function available from the <strong>Web Service→Secondary\r
+Structure Prediction→JNet Secondary Structure \r
+Prediction</strong> menu does two different kinds of prediction, \r
+dependent upon the currently selected region:</p> \r
+<ul>\r
+<li>If nothing is selected, and the displayed sequences appear to\r
+be aligned, then a JNet prediction will be run for the first\r
+sequence in the alignment, using the current\r
+alignment. Otherwise the first sequence will be submitted for prediction.\r
+</li>\r
+<li>If\r
+just one sequence (or a region on one sequence) has been selected,\r
+it will be submitted to the automatic JNet prediction server\r
+for homolog detection and prediction.\r
+</li>\r
+<li>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\r
+<strong>first</strong> sequence selected in the set (that is, the one\r
+nearest the top of the alignment window).\r
+</li> \r
+</ul>\r
+<p>The result of a JNet prediction for a sequence is a new annotated\r
+ alignment window:</p>\r
+<img src="jnetprediction.gif">\r
+<p>\r
+The sequence for which the prediction was made is the first one in the\r
+alignment. If a sequence based prediction was made then the remaining\r
+sequences in the alignment are the aligned parts of homologs which\r
+were used to construct a sequence profile for the prediction. If the\r
+prediction was made using a multiple alignment, then the original\r
+multiple alignment will be returned, annotated with the prediction.\r
+</p>\r
+The annotation bars below the alignment are as follows:</p>\r
+<ul>\r
+<li>Lupas_21, Lupas_14, Lupas_28<br>\r
+<em>Coiled-coil predictions for the sequence. These are binary\r
+predictions for each location.</em></li>\r
+<li>JNETSOL25,JNETSOL5,JNETSOL0<br>\r
+<em>Solvent accessibility predictions - binary predictions of 25%, 5%\r
+or 0% solvent accessibility.</em></li>\r
+<li>JNetPRED<br>\r
+<em>The consensus prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>JNetCONF<br>\r
+<em>The confidence estimate for the prediction. High values mean high\r
+confidence. prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>JNetALIGN<br>\r
+<em>Alignment based prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>JNetHMM<br>\r
+<em>HMM profile based prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>jpred<br>\r
+<em>Jpred prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>JNETPSSM<br>\r
+<em>PSSM based prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>JNETFREQ<br>\r
+<em>Amino Acid frequency based prediction - helices are marked as red tubes, and\r
+sheets as dark green arrows.</em></li>\r
+<li>JNETJURY<br>\r
+<em>A '*' in this annotation indicates that the JNETJURY was invoked\r
+to rationalise significantly different primary predictions.</em></li>\r
+</ul>\r
+</p>\r
+</body>\r
+</html>\r
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