Partition functions for locally stable secondary structures

Collaboration diagram for Partition functions for locally stable secondary structures:

Files
file	LPfold.h
	Function declarations of partition function variants of the Lfold algorithm.

Functions
void	update_pf_paramsLP (int length)
plist *	pfl_fold (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup)
	Compute partition functions for locally stable secondary structures. More...
plist *	pfl_fold_par (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, struct plist **dpp2, FILE *pUfp, FILE *spup, pf_paramT *parameters)
	Compute partition functions for locally stable secondary structures.
void	putoutpU_prob (double **pU, int length, int ulength, FILE *fp, int energies)
	Writes the unpaired probabilities (pU) or opening energies into a file. More...
void	putoutpU_prob_bin (double **pU, int length, int ulength, FILE *fp, int energies)
	Writes the unpaired probabilities (pU) or opening energies into a binary file. More...

Detailed Description

Function Documentation

void update_pf_paramsLP

(

int

length

)

Parameters

length

plist* pfl_fold	(	char *	sequence,
		int	winSize,
		int	pairSize,
		float	cutoffb,
		double **	pU,
		struct plist **	dpp2,
		FILE *	pUfp,
		FILE *	spup
	)

Compute partition functions for locally stable secondary structures.

pfl_fold computes partition functions for every window of size 'winSize' possible in a RNA molecule, allowing only pairs with a span smaller than 'pairSize'. It returns the mean pair probabilities averaged over all windows containing the pair in 'pl'. 'winSize' should always be >= 'pairSize'. Note that in contrast to Lfold(), bases outside of the window do not influence the structure at all. Only probabilities higher than 'cutoffb' are kept.

If 'pU' is supplied (i.e is not the NULL pointer), pfl_fold() will also compute the mean probability that regions of length 'u' and smaller are unpaired. The parameter 'u' is supplied in 'pup[0][0]'. On return the 'pup' array will contain these probabilities, with the entry on 'pup[x][y]' containing the mean probability that x and the y-1 preceding bases are unpaired. The 'pU' array needs to be large enough to hold n+1 float* entries, where n is the sequence length.

If an array dpp2 is supplied, the probability of base pair (i,j) given that there already exists a base pair (i+1,j-1) is also computed and saved in this array. If pUfp is given (i.e. not NULL), pU is not saved but put out imediately. If spup is given (i.e. is not NULL), the pair probabilities in pl are not saved but put out imediately.

Parameters

sequence	RNA sequence
winSize	size of the window
pairSize	maximum size of base pair
cutoffb	cutoffb for base pairs
pU	array holding all unpaired probabilities
dpp2	array of dependent pair probabilities
pUfp	file pointer for pU
spup	file pointer for pair probabilities

Returns

list of pair probabilities

void putoutpU_prob	(	double **	pU,
		int	length,
		int	ulength,
		FILE *	fp,
		int	energies
	)

Writes the unpaired probabilities (pU) or opening energies into a file.

Can write either the unpaired probabilities (accessibilities) pU or the opening energies -log(pU)kT into a file

Parameters

pU	pair probabilities
length	length of RNA sequence
ulength	maximum length of unpaired stretch
fp	file pointer of destination file
energies	switch to put out as opening energies

void putoutpU_prob_bin	(	double **	pU,
		int	length,
		int	ulength,
		FILE *	fp,
		int	energies
	)

Writes the unpaired probabilities (pU) or opening energies into a binary file.

Can write either the unpaired probabilities (accessibilities) pU or the opening energies -log(pU)kT into a file

Parameters

pU	pair probabilities
length	length of RNA sequence
ulength	maximum length of unpaired stretch
fp	file pointer of destination file
energies	switch to put out as opening energies