Partition Function for two hybridized Sequences
[Calculate Secondary Structures of two RNAs upon Dimerization, Calculating Partition Functions and Pair Probabilities]

Partition Function Cofolding. More...

Collaboration diagram for Partition Function for two hybridized Sequences:

Files
file	part_func_co.h
	Partition function for two RNA sequences.
Functions
cofoldF	co_pf_fold (char sequence, char structure)
	Calculate partition function and base pair probabilities.
cofoldF	co_pf_fold_par (char sequence, char structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)
	Calculate partition function and base pair probabilities.
double *	export_co_bppm (void)
	Get a pointer to the base pair probability array.
void	free_co_pf_arrays (void)
	Free the memory occupied by co_pf_fold().
void	update_co_pf_params (int length)
	Recalculate energy parameters.
void	update_co_pf_params_par (int length, pf_paramT *parameters)
	Recalculate energy parameters.
void	compute_probabilities (double FAB, double FEA, double FEB, struct plist prAB, struct plist prA, struct plist *prB, int Alength)
	Compute Boltzmann probabilities of dimerization without homodimers.
ConcEnt *	get_concentrations (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)
	Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers.
Variables
int	mirnatog
	Toggles no intrabp in 2nd mol.
double	F_monomer [2]
	Free energies of the two monomers.

Detailed Description

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 bernhart:2006 for further details.

Function Documentation

cofoldF co_pf_fold	(	char *	sequence,
		char *	structure
	)

Calculate partition function and base pair probabilities.

This is the cofold partition function folding. The second molecule starts at the cut_point nucleotide.

Note:: OpenMP: Since this function relies on the global parameters do_backtrack, dangles, temperature and pf_scale it is not threadsafe according to concurrent changes in these variables! Use co_pf_fold_par() instead to circumvent this issue.

See also:: co_pf_fold_par()

Parameters:

	sequence	Concatenated RNA sequences
	structure	Will hold the structure or constraints

Returns:: cofoldF structure containing a set of energies needed for concentration computations.

cofoldF co_pf_fold_par	(	char *	sequence,
		char *	structure,
		pf_paramT *	parameters,
		int	calculate_bppm,
		int	is_constrained
	)

Calculate partition function and base pair probabilities.

This is the cofold partition function folding. The second molecule starts at the cut_point nucleotide.

See also:: get_boltzmann_factors(), co_pf_fold()

Parameters:

	sequence	Concatenated RNA sequences
	structure	Pointer to the structure constraint
	parameters	Data structure containing the precalculated Boltzmann factors
	calculate_bppm	Switch to turn Base pair probability calculations on/off (0==off)
	is_constrained	Switch to indicate that a structure contraint is passed via the structure argument (0==off)

Returns:: cofoldF structure containing a set of energies needed for concentration computations.

double* export_co_bppm ( void )

Get a pointer to the base pair probability array.

Accessing the base pair probabilities for a pair (i,j) is achieved by

FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j];

See also:: get_iindx()

Returns:: A pointer to the base pair probability array

void update_co_pf_params ( int length )

Recalculate energy parameters.

This function recalculates all energy parameters given the current model settings.

Note:: This function relies on the global variables pf_scale, dangles and temperature. Thus it might not be threadsafe in certain situations. Use update_co_pf_params_par() instead.

See also:: get_boltzmann_factors(), update_co_pf_params_par()

Parameters:

length

Length of the current RNA sequence

void update_co_pf_params_par	(	int	length,
		pf_paramT *	parameters
	)

Recalculate energy parameters.

This function recalculates all energy parameters given the current model settings. It's second argument can either be NULL or a data structure containing the precomputed Boltzmann factors. In the first scenario, the necessary data structure will be created automatically according to the current global model settings, i.e. this mode might not be threadsafe. However, if the provided data structure is not NULL, threadsafety for the model parameters dangles, pf_scale and temperature is regained, since their values are taken from this data structure during subsequent calculations.

See also:: get_boltzmann_factors(), update_co_pf_params()

Parameters:

	length	Length of the current RNA sequence
	parameters	data structure containing the precomputed Boltzmann factors

void compute_probabilities	(	double	FAB,
		double	FEA,
		double	FEB,
		struct plist *	prAB,
		struct plist *	prA,
		struct plist *	prB,
		int	Alength
	)

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 assign_plist_from_pr(), the dimer probabilities 'prAB' are modified in place.

Parameters:

	FAB	free energy of dimer AB
	FEA	free energy of monomer A
	FEB	free energy of monomer B
	prAB	pair probabilities for dimer
	prA	pair probabilities monomer
	prB	pair probabilities monomer
	Alength	Length of molecule A

ConcEnt* get_concentrations	(	double	FEAB,
		double	FEAA,
		double	FEBB,
		double	FEA,
		double	FEB,
		double *	startconc
	)

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 cofoldF struct.

Parameters:

	FEAB	Free energy of AB dimer (FcAB entry)
	FEAA	Free energy of AA dimer (FcAB entry)
	FEBB	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]

Returns:: ConcEnt array containing the equilibrium energies and start concentrations

Partition Function for two hybridized Sequences [Calculate Secondary Structures of two RNAs upon Dimerization, Calculating Partition Functions and Pair Probabilities]

Files

Functions

Variables

Detailed Description

Function Documentation

Partition Function for two hybridized Sequences
[Calculate Secondary Structures of two RNAs upon Dimerization, Calculating Partition Functions and Pair Probabilities]