RNAlib-2.4.5
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Partition Function Cofolding. More...
Partition Function Cofolding.
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)
Files | |
file | concentrations.h |
Concentration computations for RNA-RNA interactions. | |
file | part_func_co.h |
Partition function for two RNA sequences. | |
file | part_func_up.h |
Implementations for accessibility and RNA-RNA interaction as a stepwise process. | |
Data Structures | |
struct | vrna_dimer_pf_s |
Data structure returned by vrna_pf_dimer() More... | |
Typedefs | |
typedef struct vrna_dimer_pf_s | vrna_dimer_pf_t |
Typename for the data structure that stores the dimer partition functions, vrna_dimer_pf_s, as returned by vrna_pf_dimer() | |
typedef struct vrna_dimer_pf_s | cofoldF |
Backward compatibility typedef for vrna_dimer_pf_s. | |
Functions | |
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) |
Compute Boltzmann probabilities of dimerization without homodimers. More... | |
vrna_dimer_pf_t | vrna_pf_dimer (vrna_fold_compound_t *vc, char *structure) |
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More... | |
vrna_dimer_pf_t | vrna_pf_co_fold (const char *seq, char *structure, vrna_ep_t **pl) |
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers. More... | |
Variables | |
int | mirnatog |
Toggles no intrabp in 2nd mol. | |
double | F_monomer [2] |
Free energies of the two monomers. | |
typedef struct vrna_dimer_conc_s | vrna_dimer_conc_t |
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 |
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) |
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. More... | |
struct vrna_dimer_pf_s |
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 | ||
) |
#include <ViennaRNA/equilibrium_probs.h>
Compute Boltzmann probabilities of dimerization without homodimers.
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.
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 | ||
) |
#include <ViennaRNA/part_func.h>
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers.
This is the cofold partition function folding.
vc | the fold compound data structure |
structure | Will hold the structure or constraints |
vrna_dimer_pf_t vrna_pf_co_fold | ( | const char * | seq, |
char * | structure, | ||
vrna_ep_t ** | pl | ||
) |
#include <ViennaRNA/part_func_co.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.
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) |
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.
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 |