Partition Function for Two Hybridized Sequences

To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed. See Bernhart et al. [2006] for further details.

As for folding one RNA molecule, this computes the partition function of all possible structures and the base pair probabilities. Uses the same global #pf_scale variable to avoid overflows.

After computing the partition functions of all possible dimeres one can compute the probabilities of base pairs, the concentrations out of start concentrations and sofar and soaway.

Dimer formation is inherently concentration dependent. Given the free energies of the monomers A and B and dimers AB, AA, and BB one can compute the equilibrium concentrations, given input concentrations of A and B, see e.g. Dimitrov & Zuker (2004)

typedef struct vrna_dimer_conc_s vrna_dimer_conc_t: #include <ViennaRNA/concentrations.h>
Typename for the data structure that stores the dimer concentrations, vrna_dimer_conc_s, as required by vrna_pf_dimer_concentration()

typedef struct vrna_dimer_conc_s ConcEnt: #include <ViennaRNA/concentrations.h>
Backward compatibility typedef for vrna_dimer_conc_s.

vrna_dimer_conc_t *vrna_pf_dimer_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params)

#include <ViennaRNA/concentrations.h>

Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers.

This function takes an array ‘startconc’ of input concentrations with alternating entries for the initial concentrations of molecules A and B (terminated by two zeroes), then computes the resulting equilibrium concentrations from the free energies for the dimers. Dimer free energies should be the dimer-only free energies, i.e. the FcAB entries from the vrna_dimer_pf_t struct.

Parameters

FcAB – Free energy of AB dimer (FcAB entry)
FcAA – Free energy of AA dimer (FcAB entry)
FcBB – Free energy of BB dimer (FcAB entry)
FEA – Free energy of monomer A
FEB – Free energy of monomer B
startconc – List of start concentrations [a0],[b0],[a1],[b1],…,[an][bn],[0],[0]
exp_params – The precomputed Boltzmann factors

Returns

vrna_dimer_conc_t array containing the equilibrium energies and start concentrations

double *vrna_equilibrium_constants(const double *dG_complexes, const double *dG_strands, const unsigned int **A, double kT, size_t strands, size_t complexes): #include <ViennaRNA/concentrations.h>

vrna_dimer_pf_t vrna_pf_co_fold(const char *seq, char *structure, vrna_ep_t **pl)

#include <ViennaRNA/part_func.h>

Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers.

This simplified interface to vrna_pf_dimer() computes the partition function and, if required, base pair probabilities for an RNA-RNA interaction using default options. Memory required for dynamic programming (DP) matrices will be allocated and free’d on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing.