4 <meta charset="ISO-8859-1">
5 <title>RNAalifold Web Service</title>
8 <strong>RNAalifold RNA Alignment Secondary Structure
9 Prediction Service</strong>
11 RNAalifold analyses the pattern of base pair conservation in an RNA
12 alignment in order to predict a consensus secondary structure.<br>It
13 is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
14 RNA</a> Secondary Structure Prediction and Comparison Package. It was
15 described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
16 Gruber, and Peter F. Stadler, <em>RNAalifold: Improved consensus
17 structure prediction for RNA alignments</em> (BMC Bioinformatics, 9:474,
18 2008). Download the paper at <a
19 href="http://www.biomedcentral.com/1471-2105/9/474">http://www.biomedcentral.com/1471-2105/9/474</a>.
22 <strong>Running RNAalifold from Jalview</strong><br />
24 Jalview supports access to RNAalifold services provided by JABA 2.1
25 servers. To enable RNAalifold predictions for an RNA alignment, go to
26 <strong>Webservices→Secondary Structure Prediction</strong> and
27 select <strong>RNAalifold prediction</strong> to run with current
28 defaults, and <strong>Change settings ...</strong> to adjust
29 prediction parameters. The RNA secondary structure prediction for the
30 alignment will be shown as alignment annotation, and any edits will
31 trigger the prediction to be recalculated.
33 <Strong>RNAalifold prediction parameters</Strong> <br /> JABAWS and
34 Jalview only provide access to a selection of the RNAalifold
35 arguments. For a full description, see the documentation at <a
36 href="http://www.tbi.univie.ac.at/RNA/RNAalifold.html">http://www.tbi.univie.ac.at/RNA/RNAalifold.html</a>.
39 <strong>Supported Arguments which give alternate structures</strong>
42 <em>Partition Function (-p)</em><br /> Calculate the Partition
43 Function and base pairing probability matrix in addition to the mfe
44 structure. A coarse representation of the pair probabilities in the
45 from of a pseudo bracket notation, as well as the centroid structure
46 derived from the pair probabilities are displayed. The most likely
47 base pairings are stored in a separate file by RNAalifold and
48 represented in Jalview by a bar graph annotation line labeled
49 'Contact Probabilities'.
52 <em>Maximum Expected Accuracy Structure (--MEA)</em><br /> Calculate
53 an MEA structure where the expected Accuracy is computed from the base
54 pair probabilities. A more detailed description can be found in the <strong>RNAfold</strong>
55 program documentation at <a
56 href="http://www.tbi.univie.ac.at/RNA/RNAfold.html">http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>.
59 <strong>Example RNAalifold Structure Annotation rows</strong>
62 <img src="RNAalifoldAnnotationRows.png" width="500" height="216">