Partition Function Cofolding. More…
// typedefs typedef struct vrna_dimer_conc_s vrna_dimer_conc_t typedef struct vrna_dimer_conc_s ConcEnt typedef struct vrna_dimer_pf_s vrna_dimer_pf_t typedef struct vrna_dimer_pf_s cofoldF // structs struct vrna_dimer_pf_s // global variables int mirnatog double F_monomer[2] // global functions 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 ) void vrna_pf_dimer_probs ( double FAB, double FA, double FB, vrna_ep_t* prAB, const vrna_ep_t* prA, const vrna_ep_t* prB, int Alength, const vrna_exp_param_t* exp_params ) vrna_dimer_pf_t vrna_pf_dimer ( vrna_fold_compound_t* vc, char* structure ) vrna_dimer_pf_t vrna_pf_co_fold ( const char* seq, char* structure, vrna_ep_t** pl )
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 [1] 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.
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.
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
typedef struct vrna_dimer_conc_s ConcEnt
typedef struct vrna_dimer_pf_s vrna_dimer_pf_t
typedef struct vrna_dimer_pf_s cofoldF
int mirnatog
double F_monomer [2]
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 )
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
void vrna_pf_dimer_probs ( double FAB, double FA, double FB, vrna_ep_t* prAB, const vrna_ep_t* prA, const vrna_ep_t* prB, int Alength, const vrna_exp_param_t* exp_params )
Given the pair probabilities and free energies (in the null model) for a dimer AB and the two constituent monomers A and B, compute the conditional pair probabilities given that a dimer AB actually forms. Null model pair probabilities are given as a list as produced by vrna_plist_from_probs() , the dimer probabilities ‘prAB’ are modified in place.
Parameters:
FAB | free energy of dimer AB |
FA | free energy of monomer A |
FB | free energy of monomer B |
prAB | pair probabilities for dimer |
prA | pair probabilities monomer |
prB | pair probabilities monomer |
Alength | Length of molecule A |
exp_params | The precomputed Boltzmann factors |
vrna_dimer_pf_t vrna_pf_dimer ( vrna_fold_compound_t* vc, char* structure )
This is the cofold partition function folding.
SWIG Wrapper Notes This function is attached as method pf_dimer() to objects of type fold_compound
Parameters:
vc | the fold compound data structure |
structure | Will hold the structure or constraints |
Returns:
vrna_dimer_pf_t structure containing a set of energies needed for concentration computations.
See also:
vrna_fold_compound() for how to retrieve the necessary data structure
vrna_dimer_pf_t vrna_pf_co_fold ( const char* seq, char* structure, vrna_ep_t** pl )
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.
Parameters:
seq | Two concatenated RNA sequences with a delimiting ‘&’ in between |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_ep_t to store pairing probabilities (Maybe NULL) |
Returns:
vrna_dimer_pf_t structure containing a set of energies needed for concentration computations.
Note
In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_pf_dimer() , and the data structure vrna_fold_compound_t instead.
See also: