pknotsRG 1.3

pknotsRG 1.3 is released as a flexible and useful 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.