<tocitem text="What's new" target="new" expand="true">
<tocitem text="Protein Disorder Prediction" target="disorder"/>
<tocitem text="Alignment Conservation Analysis" target="aacon"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
<tocitem text="Viewing RNA structure" target="varna" />
<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
<tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
</tocitem>
<tocitem text="Secondary Structure Prediction" target="jnet"/>
+ <tocitem text="RNAalifold RNA Secondary Structure Prediction" target="rnaalifold"/>
<tocitem text="Protein Disorder Prediction" target="disorder"/>
<tocitem text="Alignment Conservation Analysis" target="aacon"/>
<tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
--- /dev/null
+<!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 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>
+
+</body>
+</html>
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git://source.jalview.org / jalview.git / commitdiff
