Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints. More…
// global functions int vrna_sc_add_SHAPE_deigan ( vrna_fold_compound_t* vc, const double* reactivities, double m, double b, unsigned int options ) int vrna_sc_add_SHAPE_deigan_ali ( vrna_fold_compound_t* vc, const char** shape_files, const int* shape_file_association, double m, double b, unsigned int options ) int vrna_sc_add_SHAPE_zarringhalam ( vrna_fold_compound_t* vc, const double* reactivities, double b, double default_value, const char* shape_conversion, unsigned int options ) int vrna_sc_SHAPE_to_pr ( const char* shape_conversion, double* values, int length, double default_value )
int vrna_sc_add_SHAPE_deigan ( vrna_fold_compound_t* vc, const double* reactivities, double m, double b, unsigned int options )
This approach of SHAPE directed RNA folding uses the simple linear ansatz
to convert SHAPE reactivity values to pseudo energies whenever a nucleotide :math:` i ` contributes to a stacked pair. A positive slope :math:` m ` penalizes high reactivities in paired regions, while a negative intercept :math:` b ` results in a confirmatory ` bonus ‘ free energy for correctly predicted base pairs. Since the energy evaluation of a base pair stack involves two pairs, the pseudo energies are added for all four contributing nucleotides. Consequently, the energy term is applied twice for pairs inside a helix and only once for pairs adjacent to other structures. For all other loop types the energy model remains unchanged even when the experimental data highly disagrees with a certain motif.
SWIG Wrapper Notes This function is attached as method sc_add_SHAPE_deigan() to objects of type fold_compound
Parameters:
vc | 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 |
Returns:
1 on successful extraction of the method, 0 on errors
See also:
For further details, we refer to [4] .
vrna_sc_remove() , vrna_sc_add_SHAPE_zarringhalam() , vrna_sc_minimize_pertubation()
int vrna_sc_add_SHAPE_deigan_ali ( vrna_fold_compound_t* vc, const char** shape_files, const int* shape_file_association, double m, double b, unsigned int options )
SWIG Wrapper Notes This function is attached as method sc_add_SHAPE_deigan_ali() to objects of type fold_compound
Parameters:
vc | 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 |
Returns:
1 on successful extraction of the method, 0 on errors
int vrna_sc_add_SHAPE_zarringhalam ( vrna_fold_compound_t* vc, const double* reactivities, double b, double default_value, const char* shape_conversion, unsigned int options )
This method first converts the observed SHAPE reactivity of nucleotide :math:` i ` into a probability :math:` q_i ` that position :math:` i ` is unpaired by means of a non-linear map. Then pseudo-energies of the form
are computed, where :math:` x_i=0 ` if position :math:` i ` is unpaired and :math:` x_i=1 ` if :math:` i ` is paired in a given secondary structure. The parameter :math:` beta ` serves as scaling factor. The magnitude of discrepancy between prediction and experimental observation is represented by :math:` |x_i - q_i| ` .
SWIG Wrapper Notes This function is attached as method sc_add_SHAPE_zarringhalam() to objects of type fold_compound
Parameters:
vc | The vrna_fold_compound_t the soft constraints are associated with |
reactivities | A vector of normalized SHAPE reactivities |
b | The scaling factor :math:` beta ` of the conversion function |
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 |
Returns:
1 on successful extraction of the method, 0 on errors
See also:
For further details, we refer to [22]
vrna_sc_remove() , vrna_sc_add_SHAPE_deigan() , vrna_sc_minimize_pertubation()
int vrna_sc_SHAPE_to_pr ( const char* shape_conversion, double* values, int length, double default_value )
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.
Parameters:
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 |
See also: