pknotsRG RNA folding and thermodynamic matching
Download

pknotsRG Ranking & Summary

pknotsRG Tags

fold rna RNA computation RNA folder pseudoknot folder pseudoknot

pknotsRG Description

RNA folding and thermodynamic matching pknotsRG is a free and easy to use command line based tool for folding RNA secondary structures, including the class of simple recursive pseudoknots.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. What's New in This Release: · no need for garbage collector library anymore · interactive mode · support for fasta file input · new option -w: sliding window · new option -S: output width for structures

pknotsRG Related Software