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<!DOCTYPE html>
<html>
<head>
<title>RNAalifold Web Service</title>
</head>
<body>
- <strong>RNAalifold RNA Alignment Secondary Structure
- Prediction Service</strong>
- <p>
- RNAalifold 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>. (<a
- href=http://www.biomedcentral.com/1471-2105/9/474>BMC
- Bioinformatics, 9:474, 2008</a>).
- </p>
- <p>
- <strong>Example RNAalifold Output</strong><br />
- RNAalifold prints a consensus alignment and mfe structure to stdout with its
- associated energy. Depending on the arguments given, other information such as
- alternate structures are displayed below while base pairing probabilities (-p or --MEA
- options) are stored in a separate 'alifold.out' file.<br />
- <pre><br />
-G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 + -7.36)
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
- frequency of mfe structure in ensemble 0.765639
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 + -7.36}
-(.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}
-
-Alifold.out
- 6 89 9 99.2% 0.023 CG:29 GC:14 UA:9
- 4 91 11 99.1% 0.028 CG:20 GC:11 UG:2 UA:17
- 3 92 18 96.9% 0.090 CG:5 GC:2 GU:1 UG:4 AU:6 UA:25
- 35 46 3 93.3% 0.195 CG:31 GC:16 UG:2 AU:5 UA:4
- 36 45 10 93.6% 0.185 CG:16 GC:6 GU:1 UG:2 AU:8 UA:18
- .
- .
- .
- </pre>
- </p>
- <p>
- <strong>Running RNAalifold from Jalview</strong><br />
- To run RNAalifold go to <strong>Webservices→RNA Structure Prediction</strong>
- and choose <strong>RNAalifold Defaults</strong> to run with no arguments or
- <strong>edit settings and run ...</strong> to adjust the parameters before running.
- Details of all the RNAalifold parameters can be found in the
- <a href=http://www.tbi.univie.ac.at/RNA/man/RNAalifold.html>RNAalifold Manpage</a>.
- JABAWS and Jalview support a selection of the RNAalifold arguments only.
- </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 from of a psuedo
- 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 labelled '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 is found in the <a href=http://www.tbi.univie.ac.at/RNA/man/RNAfold.html>
- RNAfold documentation</a>.
- </p>
- <p><strong>Example RNAalifold Structure Annotation rows</strong><p>
-
- <div align="center">
- <img src="RNAalifoldAnnotationRows.png" width="500" height="216"></div>
-
+ <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>
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+</html>
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