From: Daniel Barton Date: Sat, 31 Aug 2013 16:42:19 +0000 (+0100) Subject: Brief html documentation entry for RNAalifold under webServices X-Git-Tag: Jalview_2_9~200^2~21^2~15 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e47d4dbf50727507632a3fe1c755e3141252ead7;p=jalview.git Brief html documentation entry for RNAalifold under webServices --- diff --git a/help/help.jhm b/help/help.jhm index b850b79..aaaaaf8 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -37,6 +37,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 0d2e096..e27d41a 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -22,6 +22,7 @@ + @@ -65,6 +66,7 @@ + diff --git a/help/html/webServices/RNAalifold.html b/help/html/webServices/RNAalifold.html new file mode 100644 index 0000000..ac9df34 --- /dev/null +++ b/help/html/webServices/RNAalifold.html @@ -0,0 +1,74 @@ + + + + +RNAalifold Web Service + + + RNAalifold RNA Alignment Secondary Structure + Prediction Service +

+ RNAalifold 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). +

+

+ 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
+ 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

+

+ 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'. +

+

+ 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. +

+

Example RNAalifold Structure Annotation rows

+ +

+
+ + + \ No newline at end of file diff --git a/help/html/webServices/RNAalifoldAnnotationRows.png b/help/html/webServices/RNAalifoldAnnotationRows.png new file mode 100644 index 0000000..5077d19 Binary files /dev/null and b/help/html/webServices/RNAalifoldAnnotationRows.png differ diff --git a/lib/min-jabaws-client-3.0.0.jar b/lib/min-jabaws-client-3.0.0.jar index 531b8d1..bfa91f0 100644 Binary files a/lib/min-jabaws-client-3.0.0.jar and b/lib/min-jabaws-client-3.0.0.jar differ