Implementations to predict pseudoknotted structures. More...
Implementations to predict pseudoknotted structures.
Files | |
file | pk_plex.h |
Heuristics for two-step pseudoknot forming interaction predictions. | |
Data Structures | |
struct | vrna_pk_plex_result_s |
A result of the RNA PKplex interaction prediction. More... | |
Typedefs | |
typedef int() | vrna_callback_pk_plex_score(const short *pt, int start_5, int end_5, int start_3, int end_3, void *data) |
Pseudoknot loop scoring function prototype. More... | |
typedef struct vrna_pk_plex_option_s * | vrna_pk_plex_opt_t |
RNA PKplex options object. More... | |
typedef struct vrna_pk_plex_result_s | vrna_pk_plex_t |
Convenience typedef for results of the RNA PKplex prediction. More... | |
Functions | |
vrna_pk_plex_t * | vrna_pk_plex (vrna_fold_compound_t *fc, const int **accessibility, vrna_pk_plex_opt_t options) |
Predict Pseudoknot interactions in terms of a two-step folding process. More... | |
int ** | vrna_pk_plex_accessibility (const char *sequence, unsigned int unpaired, double cutoff) |
Obtain a list of opening energies suitable for PKplex computations. More... | |
vrna_pk_plex_opt_t | vrna_pk_plex_opt_defaults (void) |
Default options for PKplex algorithm. More... | |
vrna_pk_plex_opt_t | vrna_pk_plex_opt (unsigned int delta, unsigned int max_interaction_length, int pk_penalty) |
Simple options for PKplex algorithm. More... | |
vrna_pk_plex_opt_t | vrna_pk_plex_opt_fun (unsigned int delta, unsigned int max_interaction_length, vrna_callback_pk_plex_score *scoring_function, void *scoring_data) |
Simple options for PKplex algorithm. More... | |
struct vrna_pk_plex_result_s |
A result of the RNA PKplex interaction prediction.
typedef int() vrna_callback_pk_plex_score(const short *pt, int start_5, int end_5, int start_3, int end_3, void *data) |
#include <ViennaRNA/pk_plex.h>
Pseudoknot loop scoring function prototype.
This function is used to evaluate a formed pseudoknot (PK) interaction in vrna_pk_plex(). It is supposed to take a PK-free secondary structure as input and coordinates of an additional interaction site. From this data, the energy (penalty) to score the PK loop is derived and returned in decakal/mol. Upon passing zero in any of the interaction site coordinates (start_5
, end_5
, start_3
, end_3
) or a NULL pointer in pt
, the function must return a PK loop score. This minimum PK loop score is used in the first phase of the heuristic implemented in vrna_pk_plex() to assess whether a particular interaction is further taken into account in a later, more thorough evaluation step.
The simplest scoring function would simply return a constant score for any PK loop, no matter what type of loop is formed and how large the loop is. This is the default if vrna_pk_plex_opt_defaults() or vrna_pk_plex_opt() is used to generate options for vrna_pk_plex().
pt | The secondary structure (without pseudoknot) in pair table notation |
start_5 | The start coordinate of the 5' site of the pseudoknot interaction |
end_5 | The end coordinate of the 5' site of the pseudoknot interaction |
start_3 | The start coordinate of the 3' site of the pseudoknot interaction |
end_3 | The end coordinate of the 3' site of the pseudoknot interaction |
data | An arbitrary data structure passed from the calling function |
typedef struct vrna_pk_plex_option_s* vrna_pk_plex_opt_t |
#include <ViennaRNA/pk_plex.h>
RNA PKplex options object.
typedef struct vrna_pk_plex_result_s vrna_pk_plex_t |
#include <ViennaRNA/pk_plex.h>
Convenience typedef for results of the RNA PKplex prediction.
vrna_pk_plex_t * vrna_pk_plex | ( | vrna_fold_compound_t * | fc, |
const int ** | accessibility, | ||
vrna_pk_plex_opt_t | options | ||
) |
#include <ViennaRNA/pk_plex.h>
Predict Pseudoknot interactions in terms of a two-step folding process.
Computes simple pseudoknot interactions according to the PKplex algorithm. This simple heuristic first compiles a list of potential interaction sites that may form a pseudoknot. The resulting candidate interactions are then fixed and an PK-free MFE structure for the remainder of the sequence is computed.
The accessibility
argument is a list of opening energies for potential interaction sites. It is used in the first step of the algorithm to identify potential interactions. Upon passing NULL, the opening energies are determined automatically based on the current model settings.
Depending on the options
, the function can return the MFE (incl. PK loops) or suboptimal structures within an energy band around the MFE. The PK loop is internally scored by a scoring function that in the simplest cases assigns a constant value for each PK loop. More complicated scoring functions can be passed as well, see vrna_callback_pk_plex_score and vrna_pk_plex_opt_fun().
The function returns NULL on any error. Otherwise, a list of structures and interaction coordinates with corresponding energy contributions is returned. If no PK-interaction that satisfies the options is found, the list only consists of the PK-free MFE structure.
fc | fold compound with the input sequence and model settings |
accessibility | An array of opening energies for the implemented heuristic (maybe NULL) |
options | An vrna_pk_plex_opt_t options data structure that determines the algorithm parameters |
int ** vrna_pk_plex_accessibility | ( | const char * | sequence, |
unsigned int | unpaired, | ||
double | cutoff | ||
) |
#include <ViennaRNA/pk_plex.h>
Obtain a list of opening energies suitable for PKplex computations.
sequence | The RNA sequence |
unpaired | The maximum number of unpaired nucleotides, i.e. length of interaction |
cutoff | A cutoff value for unpaired probabilities |
vrna_pk_plex_opt_t vrna_pk_plex_opt_defaults | ( | void | ) |
#include <ViennaRNA/pk_plex.h>
Default options for PKplex algorithm.
vrna_pk_plex_opt_t vrna_pk_plex_opt | ( | unsigned int | delta, |
unsigned int | max_interaction_length, | ||
int | pk_penalty | ||
) |
#include <ViennaRNA/pk_plex.h>
Simple options for PKplex algorithm.
delta | Size of energy band around MFE for suboptimal results in dekacal/mol |
max_interaction_length | Maximum length of interaction |
pk_penalty | Energy constant to score the PK forming loop |
vrna_pk_plex_opt_t vrna_pk_plex_opt_fun | ( | unsigned int | delta, |
unsigned int | max_interaction_length, | ||
vrna_callback_pk_plex_score * | scoring_function, | ||
void * | scoring_data | ||
) |
#include <ViennaRNA/pk_plex.h>
Simple options for PKplex algorithm.
delta | Size of energy band around MFE for suboptimal results in dekacal/mol |
max_interaction_length | Maximum length of interaction |
scoring_function | Energy evaluating function to score the PK forming loop |
scoring_data | An arbitrary data structure passed to the scoring function (maybe NUL) |