RNAlib-2.4.3
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compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments More...
Files | |
file | alifold.h |
Functions for comparative structure prediction using RNA sequence alignments. | |
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. More... | |
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. More... | |
void | update_alifold_params (void) |
Update the energy parameters for alifold function. More... | |
float ** | get_ribosum (const char **Alseq, int n_seq, int length) |
Retrieve a RiboSum Scoring Matrix for a given Alignment. | |
Variables | |
double | cv_fact |
This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. More... | |
double | nc_fact |
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. More... | |
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 [9] and [2].
float energy_of_alistruct | ( | const char ** | sequences, |
const char * | structure, | ||
int | n_seq, | ||
float * | energy | ||
) |
#include <ViennaRNA/alifold.h>
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) |
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 | ||
) |
#include <ViennaRNA/alifold.h>
Get pointers to (almost) all relavant arrays used in alifold's partition function computation.
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 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 ( ![]() |
pscore | A pointer to the start of a pscore list |
void update_alifold_params | ( | void | ) |
#include <ViennaRNA/alifold.h>
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
double cv_fact |
#include <ViennaRNA/alifold.h>
This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
Default is 1.
double nc_fact |
#include <ViennaRNA/alifold.h>
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.
Default is 1.