From 1835c5e890f8089213739a87321b5faa10328cdd Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 3 Jun 2014 14:34:22 +0100 Subject: [PATCH] JAL-1503 JAL-1350 rework documentation for 2.8.1 --- help/html/webServices/RNAalifold.html | 92 +++++++++++++++------------------ 1 file changed, 42 insertions(+), 50 deletions(-) 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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