Comparative structure prediction

Overview

// global variables

double cv_fact
double nc_fact

// global functions

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

int get_alipf_arrays (
    short*** S_p,
    short*** S5_p,
    short*** S3_p,
    unsigned short*** a2s_p,
    char*** Ss_p,
    FLT_OR_DBL** qb_p,
    FLT_OR_DBL** qm_p,
    FLT_OR_DBL** q1k_p,
    FLT_OR_DBL** qln_p,
    short** pscore
    )

void update_alifold_params (void)

float** get_ribosum (
    const char** Alseq,
    int n_seq,
    int length
    )

Detailed Documentation

Global Variables

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

Deprecated See vrna_md_t.cv_fact , and vrna_mfe() to avoid using global variables

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.

Deprecated See vrna_md_t.nc_fact , and vrna_mfe() to avoid using global variables

Default is 1.

Global Functions

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.

Deprecated Usage of this function is discouraged! Use vrna_eval_structure() , and vrna_eval_covar_structure() instead!

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

int get_alipf_arrays (
    short*** S_p,
    short*** S5_p,
    short*** S3_p,
    unsigned short*** a2s_p,
    char*** Ss_p,
    FLT_OR_DBL** qb_p,
    FLT_OR_DBL** qm_p,
    FLT_OR_DBL** q1k_p,
    FLT_OR_DBL** qln_p,
    short** pscore
    )
Get pointers to (almost) all relavant arrays used in alifold’s partition function computation.

Deprecated It is discouraged to use this function! The new vrna_fold_compound_t allows direct access to all necessary consensus structure prediction related variables!

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 alignment-column to sequence position mapping array
Ss_p A pointer to the ‘Ss’ array
qb_p A pointer to the Q B matrix
qm_p A pointer to the Q M matrix
q1k_p A pointer to the 5’ slice of the Q matrix ( \(q1k(k) = Q(1, k)\) )
qln_p A pointer to the 3’ slice of the Q matrix ( \(qln(l) = Q(l, n)\) )
pscore A pointer to the start of a pscore list

Returns:

Non Zero if everything went fine, 0 otherwise

Note

To obtain meaningful pointers, call alipf_fold first!

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

Deprecated Usage of this function is discouraged! The new API uses vrna_fold_compound_t to lump all folding related necessities together, including the energy parameters. Use vrna_update_fold_params() to update the energy parameters within a vrna_fold_compound_t .

float** get_ribosum (
    const char** Alseq,
    int n_seq,
    int length
    )
Retrieve a RiboSum Scoring Matrix for a given Alignment.