From: Jim Procter Date: Tue, 3 Jun 2014 13:34:22 +0000 (+0100) Subject: JAL-1503 JAL-1350 rework documentation for 2.8.1 X-Git-Tag: Release_2_8_1~4^2~5^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1835c5e890f8089213739a87321b5faa10328cdd;p=jalview.git JAL-1503 JAL-1350 rework documentation for 2.8.1 --- diff --git a/help/html/webServices/RNAalifold.html b/help/html/webServices/RNAalifold.html index ac9df34..9428dc3 100644 --- a/help/html/webServices/RNAalifold.html +++ b/help/html/webServices/RNAalifold.html @@ -8,67 +8,59 @@ RNAalifold RNA Alignment Secondary Structure Prediction Service

- RNAalifold is part of the Vienna + RNAalifold analyses the pattern of base pair conservation in an RNA + alignment in order to predict a consensus secondary structure.
It + is part of the
Vienna RNA Secondary Structure Prediction and Comparison Package. It was described in 2008 by Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler, RNAalifold: Improved consensus - structure prediction for RNA alignments. (BMC - Bioinformatics, 9:474, 2008). + structure prediction for RNA alignments (BMC Bioinformatics, 9:474, + 2008). Download the paper at http://www.biomedcentral.com/1471-2105/9/474.

- Example RNAalifold Output
- 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.
-


-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 - . - . - . -
+ Running RNAalifold from Jalview
+

+ Jalview supports access to RNAalifold services provided by JABA 2.1 + servers. To enable RNAalifold predictions for an RNA alignment, go to + Webservices→Secondary Structure Prediction and + select RNAalifold prediction to run with current + defaults, and Change settings ... 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. +

+ RNAalifold prediction parameters
JABAWS and + Jalview only provide access to a selection of the RNAalifold + arguments. For a full description, see the documentation at http://www.tbi.univie.ac.at/RNA/RNAalifold.html.

- Running RNAalifold from Jalview
- To run RNAalifold go to Webservices→RNA Structure Prediction - and choose RNAalifold Defaults to run with no arguments or - edit settings and run ... to adjust the parameters before running. - Details of all the RNAalifold parameters can be found in the - RNAalifold Manpage. - JABAWS and Jalview support a selection of the RNAalifold arguments only. + Supported Arguments which give alternate structures

-

Supported Arguments which give alternate structures

- Partition Function (-p)
- 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'. + Partition Function (-p)
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 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'.

- Maximum Expected Accuracy Structure (--MEA)
- Calculate an MEA structure where the expected Accuracy is computed from the base pair - probabilities. A more detailed description is found in the - RNAfold documentation. + Maximum Expected Accuracy Structure (--MEA)
Calculate + an MEA structure where the expected Accuracy is computed from the base + pair probabilities. A more detailed description can be found in the RNAfold + program documentation at http://www.tbi.univie.ac.at/RNA/RNAfold.html.

-

Example RNAalifold Structure Annotation rows

- -

-
- +

+ Example RNAalifold Structure Annotation rows +

+

+ +
+

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