Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints. More...
Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints.
Details for our implementation to incorporate SHAPE reactivity data to guide secondary structure prediction can be found in [21]
Files | |
file | SHAPE.h |
This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints. | |
Functions | |
int | vrna_sc_add_SHAPE_deigan (vrna_fold_compound_t *fc, const double *reactivities, double m, double b, unsigned int options) |
Add SHAPE reactivity data as soft constraints (Deigan et al. method) | |
int | vrna_sc_add_SHAPE_deigan_ali (vrna_fold_compound_t *fc, const char **shape_files, const int *shape_file_association, double m, double b, unsigned int options) |
Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method) | |
int | vrna_sc_add_SHAPE_zarringhalam (vrna_fold_compound_t *fc, const double *reactivities, double b, double default_value, const char *shape_conversion, unsigned int options) |
Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method) | |
int | vrna_sc_SHAPE_to_pr (const char *shape_conversion, double *values, int length, double default_value) |
Convert SHAPE reactivity values to probabilities for being unpaired. | |
int vrna_sc_add_SHAPE_deigan | ( | vrna_fold_compound_t * | fc, |
const double * | reactivities, | ||
double | m, | ||
double | b, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/SHAPE.h>
Add SHAPE reactivity data as soft constraints (Deigan et al. method)
This approach of SHAPE directed RNA folding uses the simple linear ansatz
to convert SHAPE reactivity values to pseudo energies whenever a nucleotide
fc | The vrna_fold_compound_t the soft constraints are associated with |
reactivities | A vector of normalized SHAPE reactivities |
m | The slope of the conversion function |
b | The intercept of the conversion function |
options | The options flag indicating how/where to store the soft constraints |
int vrna_sc_add_SHAPE_deigan_ali | ( | vrna_fold_compound_t * | fc, |
const char ** | shape_files, | ||
const int * | shape_file_association, | ||
double | m, | ||
double | b, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/SHAPE.h>
Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method)
fc | The vrna_fold_compound_t the soft constraints are associated with |
shape_files | A set of filenames that contain normalized SHAPE reactivity data |
shape_file_association | An array of integers that associate the files with sequences in the alignment |
m | The slope of the conversion function |
b | The intercept of the conversion function |
options | The options flag indicating how/where to store the soft constraints |
int vrna_sc_add_SHAPE_zarringhalam | ( | vrna_fold_compound_t * | fc, |
const double * | reactivities, | ||
double | b, | ||
double | default_value, | ||
const char * | shape_conversion, | ||
unsigned int | options | ||
) |
#include <ViennaRNA/constraints/SHAPE.h>
Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method)
This method first converts the observed SHAPE reactivity of nucleotide
are computed, where
fc | The vrna_fold_compound_t the soft constraints are associated with |
reactivities | A vector of normalized SHAPE reactivities |
b | The scaling factor ![]() |
default_value | The default value for a nucleotide where reactivity data is missing for |
shape_conversion | A flag that specifies how to convert reactivities to probabilities |
options | The options flag indicating how/where to store the soft constraints |
int vrna_sc_SHAPE_to_pr | ( | const char * | shape_conversion, |
double * | values, | ||
int | length, | ||
double | default_value | ||
) |
#include <ViennaRNA/constraints/SHAPE.h>
Convert SHAPE reactivity values to probabilities for being unpaired.
This function parses the informations from a given file and stores the result in the preallocated string sequence and the FLT_OR_DBL array values.
shape_conversion | String definining the method used for the conversion process |
values | Pointer to an array of SHAPE reactivities |
length | Length of the array of SHAPE reactivities |
default_value | Result used for position with invalid/missing reactivity values |