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RNAlgFold
This webservice is no longer available but eventually goes online at http://www.abi.techfak.de/wp/
RNAlgfold -- Predicting RNA secondary structures
... using length-dependent stochastic context-free grammars
This web-service offers a tool to predict the (pseudo-knot free) RNA secondary structure given its sequence of nucleotides (primary structure). It is not meant a stand-alone tool but to illustrate our findings from the paper given below. Accordingly, the names used (e.g. G1, G2) refer to that paper and are left here without explanation.
The underlying stochastic model has been trained on tRNA data. accordingly you can either provide your own tRNA-sequence or choose one from a database using the pull-down menu.
Primary structure to fold:
Folding Algorithm:
G2 with lengths
G2 without lengths
G1 with lengths
G1 without lengths
Notes:
Primary structure needs to be entered as word over {A,C,G,U}. (upper case only, no spaces)
The grammars are only trained on tRNA, predictions for other types of RNA may be completely wrong.
Due to the current implementation being done in Mathematica and running with low priority predictions will take up to a minute.
Details on the algorithm can be found in
"Frank Weinberg, Markus Nebel. Applying Length-Dependent Stochastic Context-Free Grammars to RNA Secondary Structure Prediction, Algorithms Vol. 4, No. 4 (2011), 223-238"
Arbeitsgruppe
Forschung
Lehre