RNA2Dfold 2.1.9: Compute MFE structure, partition function and representative sample structures of k,l neighborhoods. The program partitions the secondary structure space into (basepair)distance classes according to two fixed reference structures. It expects a sequence and two secondary structures in dot−bracket notation as its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free energy is computed. Additionally, a stochastic backtracking routine allows to produce samples of representative suboptimal secondary structures from each partition.
Keywords for this software
References in zbMATH (referenced in 2 articles )
Showing results 1 to 2 of 2.
- Senter, Evan; Dotu, Ivan; Clote, Peter: RNA folding pathways and kinetics using 2D energy landscapes (2015)
- Sauerwine, Ben; Widom, Michael: Arrhenius lifetimes of RNA structures from free energy landscapes (2011)