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 is part of the <a href="http://www.tbi.univie.ac.at/RNA/">Vienna
12 RNA</a> Secondary Structure Prediction and Comparison Package. It was
13 described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R.
14 Gruber, and Peter F. Stadler, <em>RNAalifold: Improved consensus
15 structure prediction for RNA alignments</em>. (<a
16 href=http://www.biomedcentral.com/1471-2105/9/474>BMC
17 Bioinformatics, 9:474, 2008</a>).
20 <strong>Example RNAalifold Output</strong><br />
21 RNAalifold prints a consensus alignment and mfe structure to stdout with its
22 associated energy. Depending on the arguments given, other information such as
23 alternate structures are displayed below while base pairing probabilities (-p or --MEA
24 options) are stored in a separate 'alifold.out' file.<br />
26 G_UUUCAUU___AUGACGGCCUGUGCU_UAAA__CCUCC____GAG__C________GGGUCA_G_G_UCUGAU___CUUG_______GAGAC
27 (.((((...........(((((((((........(((......)))............))))).).).))..................))))) (-19.16 = -11.80 + -7.36)
28 (.((((...........(((((((((........(((......)))............))))).).).))..................))))) [-19.32]
29 frequency of mfe structure in ensemble 0.765639
30 (.((((...........(((((((((........(((......)))............))))).).).))..................))))) -19.16 {-11.80 + -7.36}
31 (.((((...........(((((((((........(((......)))............))))).).).))..................))))) { 13.20 MEA=92.14}
34 6 89 9 99.2% 0.023 CG:29 GC:14 UA:9
35 4 91 11 99.1% 0.028 CG:20 GC:11 UG:2 UA:17
36 3 92 18 96.9% 0.090 CG:5 GC:2 GU:1 UG:4 AU:6 UA:25
37 35 46 3 93.3% 0.195 CG:31 GC:16 UG:2 AU:5 UA:4
38 36 45 10 93.6% 0.185 CG:16 GC:6 GU:1 UG:2 AU:8 UA:18
45 <strong>Running RNAalifold from Jalview</strong><br />
46 To run RNAalifold go to <strong>Webservices→RNA Structure Prediction</strong>
47 and choose <strong>RNAalifold Defaults</strong> to run with no arguments or
48 <strong>edit settings and run ...</strong> to adjust the parameters before running.
49 Details of all the RNAalifold parameters can be found in the
50 <a href=http://www.tbi.univie.ac.at/RNA/man/RNAalifold.html>RNAalifold Manpage</a>.
51 JABAWS and Jalview support a selection of the RNAalifold arguments only.
53 <p><strong>Supported Arguments which give alternate structures</strong></p>
55 <em>Partition Function (-p)</em><br />
56 Calculate the Partition Function and base pairing probability matrix in addition to the mfe
57 structure. A coarse representation of the pair probabilities in the from of a psuedo
58 bracket notation, as well as the centroid structure derived from the pair probabilities
59 are displayed. The most likely base pairings are stored in a separate file by RNAalifold
60 and represented in Jalview by a bar graph annotation line labelled 'Contact Probabilities'.
63 <em>Maximum Expected Accuracy Structure (--MEA)</em><br />
64 Calculate an MEA structure where the expected Accuracy is computed from the base pair
65 probabilities. A more detailed description is found in the <a href=http://www.tbi.univie.ac.at/RNA/man/RNAfold.html>
66 RNAfold documentation</a>.
68 <p><strong>Example RNAalifold Structure Annotation rows</strong><p>
71 <img src="RNAalifoldAnnotationRows.png" width="500" height="216"></div>