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Author: S. Janssen

KnotInFrame predicts -1 frameshift sites with simple pseudoknots. More complex knotted structures like triple crossing helices or kissing hairpins are excluded from calculation.

The prediction is based on a comparison between the minimal free energy (mfe) structure, calculated by an RNAfold like program and the mfe-structure, computed by a modified version of pknotsRG-mfe, called pknotsRG-frameshift developed by Jens Reeder and Robert Giegerich.


Short sequences up to 120 nucleotides can be predicted within 0.6sec. Genomes of 5MB can be compute in about 1h 37min.

Illustration of a programmed -1 frameshift.

Figure 1: Model for BWYV -1 frameshift [ ala:atk:ges:1999].

Additional material on the comparison with the yeast screen of [jac:bel:rak:din:2007]


Users of KnotInFrame are requested to cite :
Theis, Corinna and Reeders, Jens and Giegerich, Robert KnotInFrame: prediction of -1 ribosomal frameshift events, Nucleic Acids Research, 2008