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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
<title>RNAalifold Web Service</title>
</head>
<body>
- <strong>RNAalifold RNA Alignment Secondary Structure
- Prediction Service</strong>
- <p>
- RNAalifold analyses the pattern of base pair conservation in an RNA
- alignment in order to predict a consensus secondary structure.<br>It
- is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
- RNA</a> Secondary Structure Prediction and Comparison Package. It was
- described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
- Gruber, and Peter F. Stadler, <em>RNAalifold: Improved consensus
- structure prediction for RNA alignments</em> (BMC Bioinformatics, 9:474,
- 2008). Download the paper at <a
- href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
- </p>
- <p>
- <strong>Running RNAalifold from Jalview</strong><br />
- <p>
- Jalview supports access to RNAalifold services provided by JABA 2.1
- servers. To enable RNAalifold predictions for an RNA alignment, go to
- <strong>Webservices→Secondary Structure Prediction</strong> and
- select <strong>RNAalifold prediction</strong> to run with current
- defaults, and <strong>Change settings ...</strong> to adjust
- prediction parameters. The RNA secondary structure prediction for the
- alignment will be shown as alignment annotation, and any edits will
- trigger the prediction to be recalculated.
- <p>
- <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
- Jalview only provide access to a selection of the RNAalifold
- arguments. For a full description, see the documentation at <a
- href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
- </p>
- <p>
- <strong>Supported Arguments which give alternate structures</strong>
- </p>
- <p>
- <em>Partition Function (-p)</em><br /> Calculate the Partition
- Function and base pairing probability matrix in addition to the mfe
- structure. A coarse representation of the pair probabilities in the
- form of a pseudo bracket notation, as well as the centroid structure
- derived from the pair probabilities are displayed. The most likely
- base pairings are stored in a separate file by RNAalifold and
- represented in Jalview by a bar graph annotation line labeled
- 'Contact Probabilities'.
- </p>
- <p>
- <em>Maximum Expected Accuracy Structure (--MEA)</em><br /> Calculate
- an MEA structure where the expected Accuracy is computed from the base
- pair probabilities. A more detailed description can be found in the <strong>RNAfold</strong>
- program documentation at <a
- href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
- </p>
- <p>
- <strong>Example RNAalifold Structure Annotation rows</strong>
- <p>
- <div align="center">
- <img src="RNAalifoldAnnotationRows.png" width="500" height="216">
- </div>
- <p>
+ <strong>RNAalifold RNA Alignment Secondary Structure
+ Prediction Service</strong>
+ <p>
+ RNAalifold analyses the pattern of base pair conservation in an RNA
+ alignment in order to predict a consensus secondary structure.<br>It
+ is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
+ RNA</a> Secondary Structure Prediction and Comparison Package. It was
+ described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
+ Gruber, and Peter F. Stadler, <em>RNAalifold: Improved
+ consensus structure prediction for RNA alignments</em> (BMC
+ Bioinformatics, 9:474, 2008). Download the paper at <a
+ href="http://www.biomedcentral.com/1471-2105/9/474"
+ >http://www.biomedcentral.com/1471-2105/9/474</a>.
+ </p>
+ <p>
+ <strong>Running RNAalifold from Jalview</strong><br />
+ <p>
+ Jalview supports access to RNAalifold services provided by JABA 2.1
+ servers. To enable RNAalifold predictions for an RNA alignment, go
+ to <strong>Webservices→Secondary Structure Prediction</strong>
+ and select <strong>RNAalifold prediction</strong> to run with
+ current defaults, and <strong>Change settings ...</strong> to adjust
+ prediction parameters. The RNA secondary structure prediction for
+ the alignment will be shown as alignment annotation, and any edits
+ will trigger the prediction to be recalculated.
+ <p>
+ <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
+ Jalview only provide access to a selection of the RNAalifold
+ arguments. For a full description, see the documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html"
+ >http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
+ </p>
+ <p>
+ <strong>Supported Arguments which give alternate structures</strong>
+ </p>
+ <p>
+ <em>Partition Function (-p)</em><br /> Calculate the Partition
+ Function and base pairing probability matrix in addition to the mfe
+ structure. A coarse representation of the pair probabilities in the
+ form of a pseudo bracket notation, as well as the centroid structure
+ derived from the pair probabilities are displayed. The most likely
+ base pairings are stored in a separate file by RNAalifold and
+ represented in Jalview by a bar graph annotation line labeled
+ 'Contact Probabilities'.
+ </p>
+ <p>
+ <em>Maximum Expected Accuracy Structure (--MEA)</em><br />
+ Calculate an MEA structure where the expected Accuracy is computed
+ from the base pair probabilities. A more detailed description can be
+ found in the <strong>RNAfold</strong> program documentation at <a
+ href="http://www.tbi.univie.ac.at/RNA/RNAfold.html"
+ >http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
+ </p>
+ <p>
+ <strong>Example RNAalifold Structure Annotation rows</strong>
+ <p>
+ <div align="center">
+ <img src="RNAalifoldAnnotationRows.png" width="500" height="216">
+ </div>
+ <p>
</body>
</html>
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