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pknotsRG

Users and friends of pknotsRG. The online service of pknotsRG will be discontinued in near future. The latest version of pKiss includes the same functionality within a modern web application. Consider using pKiss for your task.


pknotsRG is a tool for folding RNA secondary structures, including the class of simple recursive pseudoknots. The program runs in O(n^4) time and O(n^2) space, therefore its application here on the BiBiserv is limited to sequences of length up to 800 bases. The energy parameters for structures containing no pseudoknots are the same as in the actual mfold 3.1. The energy for pseudoknots is computed with a model similar to that used by Rivas&Eddy in pknots. The folding temperature is fixed to 37C.
Currently, there are three different modes available:
  • pknotsRG-mfe: computes the structure of s (knotted or not) of minimal free energy.
  • pknotsRG-enf: enforces a pseudoknot: it delivers the energetically best complete structure of s that includes at least one pseudoknot somewhere.
  • pknotsRG-loc: delivers the best local pseudoknot that can be element of any structure of s, where "best" is defined by free energy per nucleotide. The rest of s remains unfolded.

NEW

All modes run also in a suboptimal mode, where all near-optimal structures up to a user defined threshold are enumerated. Suboptimals are vizualized by RNAmovies.

All programs make extensive use of Algebraic Dynamic Programing (ADP).

If you publish your work achieved with pknotsRG, please cite:
Jens Reeder and Robert Giegerich.
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics, BMC Bioinformatics, 5:104, 2004.
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Fri May 3 14:45:58 2013