-
- 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). Download the paper at http://www.biomedcentral.com/1471-2105/9/474.
-
- 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.
-
- 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 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 can be found in the RNAfold
- program documentation at http://www.tbi.univie.ac.at/RNA/RNAfold.html.
-
- Example RNAalifold Structure Annotation rows -
-
- + RNAalifold RNA Alignment Secondary Structure + Prediction Service +
+ 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). Download the paper at http://www.biomedcentral.com/1471-2105/9/474.
+
+ 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.
+
+ 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
+ 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 can be
+ found in the RNAfold program documentation at http://www.tbi.univie.ac.at/RNA/RNAfold.html.
+
+ Example RNAalifold Structure Annotation rows +
+
+ - \ No newline at end of file +