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-<!DOCTYPE html>
-<html>
-<head>
-<meta charset="ISO-8859-1">
-<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>
-</body>
-</html>
git://source.jalview.org / jalview.git / blobdiff