H/alifold.h File Reference

compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, . More...

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Functions
void	update_alifold_params (void)
	Update the energy parameters for alifold function.
float	alifold (const char *strings, char structure)
	Compute MFE and according consensus structure of an alignment of sequences.
float	circalifold (const char *strings, char structure)
	Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear.
void	free_alifold_arrays (void)
	Free the memory occupied by MFE alifold functions.
int	get_mpi (char Alseq[], int n_seq, int length, int mini)
	Get the mean pairwise identity in steps from ?to?(ident).
float **	readribosum (char *name)
	Read a ribosum or other user-defined scoring matrix.
float	energy_of_alistruct (const char *sequences, const char structure, int n_seq, float *energy)
	Calculate the free energy of a consensus structure given a set of aligned sequences.
void	encode_ali_sequence (const char sequence, short S, short s5, short s3, char ss, unsigned short as, int circ)
	Get arrays with encoded sequence of the alignment.
void	alloc_sequence_arrays (const char sequences, short S, short S5, short S3, unsigned short a2s, char *Ss, int circ)
	Allocate memory for sequence array used to deal with aligned sequences.
void	free_sequence_arrays (unsigned int n_seq, short *S, short S5, short S3, unsigned short a2s, char **Ss)
	Free the memory of the sequence arrays used to deal with aligned sequences.
float	alipf_fold_par (const char *sequences, char structure, plist *pl, pf_paramT parameters, int calculate_bppm, int is_constrained, int is_circular)
float	alipf_fold (const char *sequences, char structure, plist **pl)
	The partition function version of alifold() works in analogy to pf_fold().
float	alipf_circ_fold (const char *sequences, char structure, plist **pl)
FLT_OR_DBL *	export_ali_bppm (void)
	Get a pointer to the base pair probability array.
char *	alipbacktrack (double *prob)
	Sample a consensus secondary structure from the Boltzmann ensemble according its probability .
Variables
double	cv_fact
	This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
double	nc_fact
	This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.

Detailed Description

compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, .

..) for RNA sequence alignments

Function Documentation

void update_alifold_params ( void )

Update the energy parameters for alifold function.

Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like temperature

float alifold	(	const char **	strings,
		char *	structure
	)

Compute MFE and according consensus structure of an alignment of sequences.

This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.

Sufficient space must be allocated for 'structure' before calling alifold().

Parameters:

	strings	A pointer to a NULL terminated array of character arrays
	structure	A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE)

Returns:: The free energy score in kcal/mol

float circalifold	(	const char **	strings,
		char *	structure
	)

Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear.

Parameters:

	strings	A pointer to a NULL terminated array of character arrays
	structure	A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE)

Returns:: The free energy score in kcal/mol

int get_mpi	(	char *	Alseq[],
		int	n_seq,
		int	length,
		int *	mini
	)

Get the mean pairwise identity in steps from ?to?(ident).

Parameters:

	Alseq
	n_seq	The number of sequences in the alignment
	length	The length of the alignment
	mini

Returns:: The mean pairwise identity

float energy_of_alistruct	(	const char **	sequences,
		const char *	structure,
		int	n_seq,
		float *	energy
	)

Calculate the free energy of a consensus structure given a set of aligned sequences.

Parameters:

	sequences	The NULL terminated array of sequences
	structure	The consensus structure
	n_seq	The number of sequences in the alignment
	energy	A pointer to an array of at least two floats that will hold the free energies (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term)

Returns:: free energy in kcal/mol

void encode_ali_sequence	(	const char *	sequence,
		short *	S,
		short *	s5,
		short *	s3,
		char *	ss,
		unsigned short *	as,
		int	circ
	)

Get arrays with encoded sequence of the alignment.

this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)

Parameters:

	sequence	The gapped sequence from the alignment
	S	pointer to an array that holds encoded sequence
	s5	pointer to an array that holds the next base 5' of alignment position i
	s3	pointer to an array that holds the next base 3' of alignment position i
	ss
	as
	circ	assume the molecules to be circular instead of linear (circ=0)

void alloc_sequence_arrays	(	const char **	sequences,
		short ***	S,
		short ***	S5,
		short ***	S3,
		unsigned short ***	a2s,
		char ***	Ss,
		int	circ
	)

Allocate memory for sequence array used to deal with aligned sequences.

Note that these arrays will also be initialized according to the sequence alignment given

See also:: free_sequence_arrays()

Parameters:

	sequences	The aligned sequences
	S	A pointer to the array of encoded sequences
	S5	A pointer to the array that contains the next 5' nucleotide of a sequence position
	S3	A pointer to the array that contains the next 3' nucleotide of a sequence position
	a2s	A pointer to the array that contains the alignment to sequence position mapping
	Ss	A pointer to the array that contains the ungapped sequence
	circ	assume the molecules to be circular instead of linear (circ=0)

void free_sequence_arrays	(	unsigned int	n_seq,
		short ***	S,
		short ***	S5,
		short ***	S3,
		unsigned short ***	a2s,
		char ***	Ss
	)

Free the memory of the sequence arrays used to deal with aligned sequences.

This function frees the memory previously allocated with alloc_sequence_arrays()

See also:: alloc_sequence_arrays()

Parameters:

	n_seq	The number of aligned sequences
	S	A pointer to the array of encoded sequences
	S5	A pointer to the array that contains the next 5' nucleotide of a sequence position
	S3	A pointer to the array that contains the next 3' nucleotide of a sequence position
	a2s	A pointer to the array that contains the alignment to sequence position mapping
	Ss	A pointer to the array that contains the ungapped sequence

float alipf_fold_par	(	const char **	sequences,
		char *	structure,
		plist **	pl,
		pf_paramT *	parameters,
		int	calculate_bppm,
		int	is_constrained,
		int	is_circular
	)

Parameters:

	sequences
	structure
	pl
	parameters
	calculate_bppm
	is_constrained
	is_circular

Returns:

float alipf_fold	(	const char **	sequences,
		char *	structure,
		plist **	pl
	)

The partition function version of alifold() works in analogy to pf_fold().

Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of pair_info structs. The list is terminated by the first entry with pi.i = 0.

Parameters:

	sequences
	structure
	pl

Returns:

float alipf_circ_fold	(	const char **	sequences,
		char *	structure,
		plist **	pl
	)

Parameters:

	sequences
	structure
	pl

Returns:

FLT_OR_DBL* export_ali_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

char* alipbacktrack ( double * prob )

Sample a consensus secondary structure from the Boltzmann ensemble according its probability
.

Parameters:

prob

to be described (berni)

Returns:: A sampled consensus secondary structure in dot-bracket notation

Variable Documentation

double cv_fact

This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.

Default is 1.

double nc_fact

This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.

Default is 1.

H/alifold.h File Reference

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation