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. | |
Functions for comparative structure prediction using RNA sequence alignments.
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.
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) |
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
|
extern |
This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
Default is 1.
|
extern |
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.
Default is 1.