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24 <meta charset="ISO-8859-1">
25 <title>RNAalifold Web Service</title>
28 <strong>RNAalifold RNA Alignment Secondary Structure
29 Prediction Service</strong>
31 RNAalifold analyses the pattern of base pair conservation in an RNA
32 alignment in order to predict a consensus secondary structure.<br>It
33 is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
34 RNA</a> Secondary Structure Prediction and Comparison Package. It was
35 described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
36 Gruber, and Peter F. Stadler, <em>RNAalifold: Improved
37 consensus structure prediction for RNA alignments</em> (BMC
38 Bioinformatics, 9:474, 2008). Download the paper at <a
39 href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
42 <strong>Running RNAalifold from Jalview</strong><br />
44 Jalview supports access to RNAalifold services provided by JABA 2.1
45 servers. To enable RNAalifold predictions for an RNA alignment, go
46 to <strong>Webservices→Secondary Structure Prediction</strong>
47 and select <strong>RNAalifold prediction</strong> to run with
48 current defaults, and <strong>Change settings ...</strong> to adjust
49 prediction parameters. The RNA secondary structure prediction for
50 the alignment will be shown as alignment annotation, and any edits
51 will trigger the prediction to be recalculated.
53 <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
54 Jalview only provide access to a selection of the RNAalifold
55 arguments. For a full description, see the documentation at <a
56 href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
59 <strong>Supported Arguments which give alternate structures</strong>
62 <em>Partition Function (-p)</em><br /> Calculate the Partition
63 Function and base pairing probability matrix in addition to the mfe
64 structure. A coarse representation of the pair probabilities in the
65 form of a pseudo bracket notation, as well as the centroid structure
66 derived from the pair probabilities are displayed. The most likely
67 base pairings are stored in a separate file by RNAalifold and
68 represented in Jalview by a bar graph annotation line labeled
69 'Contact Probabilities'.
72 <em>Maximum Expected Accuracy Structure (--MEA)</em><br />
73 Calculate an MEA structure where the expected Accuracy is computed
74 from the base pair probabilities. A more detailed description can be
75 found in the <strong>RNAfold</strong> program documentation at <a
76 href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
79 <strong>Example RNAalifold Structure Annotation rows</strong>
82 <img src="RNAalifoldAnnotationRows.png" width="500" height="216">