- 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.
-
+ Running RNAalifold from Jalview
-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 - . - . - . -
+ 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
+ form 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 +
+
+ - \ No newline at end of file +