compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
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file alifold.h
compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
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.
int get_alipf_arrays (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p, short **pscore)
Get pointers to (almost) all relavant arrays used in alifold's partition function computation.
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.
compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
Consensus structures can be predicted by a modified version of the fold() algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see [6] and [2] .
◆ get_mpi()
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
◆ readribosum()
float ** readribosum
(
char *
name )
Read a ribosum or other user-defined scoring matrix.
◆ energy_of_alistruct()
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
◆ encode_ali_sequence()
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)
◆ alloc_sequence_arrays()
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)
◆ free_sequence_arrays()
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
◆ get_alipf_arrays()
int get_alipf_arrays
(
short ***
S_p ,
short ***
S5_p ,
short ***
S3_p ,
unsigned short ***
a2s_p ,
char ***
Ss_p ,
double **
qb_p ,
double **
qm_p ,
double **
q1k_p ,
double **
qln_p ,
short **
pscore
)
Get pointers to (almost) all relavant arrays used in alifold's partition function computation.
Note To obtain meaningful pointers, call alipf_fold first!
See also pf_alifold(), alipf_circ_fold()
Parameters
S_p A pointer to the 'S' array (integer representation of nucleotides)
S5_p A pointer to the 'S5' array
S3_p A pointer to the 'S3' array
a2s_p A pointer to the pair type matrix
Ss_p A pointer to the 'Ss' array
qb_p A pointer to the QB matrix
qm_p A pointer to the QM matrix
q1k_p A pointer to the 5' slice of the Q matrix ( )
qln_p A pointer to the 3' slice of the Q matrix ( )
Returns Non Zero if everything went fine, 0 otherwise
◆ cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
Default is 1.
◆ 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.