RNAlib-2.6.3
 
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Functions for comparative structure prediction using RNA sequence alignments. More...

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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.
 
void update_alifold_params (void)
 Update the energy parameters for alifold function.
 

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

Functions for comparative structure prediction using RNA sequence alignments.

Function Documentation

◆ 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.

Deprecated:
Usage of this function is discouraged! Use vrna_eval_structure(), and vrna_eval_covar_structure() instead!
Parameters
sequencesThe NULL terminated array of sequences
structureThe consensus structure
n_seqThe number of sequences in the alignment
energyA 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

◆ update_alifold_params()

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.

Variable Documentation

◆ cv_fact

double cv_fact
extern

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.

◆ nc_fact

double nc_fact
extern

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.