RNAlib-2.4.5
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Macros | |
#define | VRNA_PROBS_WINDOW_BPP 4096U |
Option flag to activate callback triggers for pairing probabilities. More... | |
#define | VRNA_PROBS_WINDOW_UP 8192U |
Option flag to activate callback triggers for unpaired probabilities. More... | |
#define | VRNA_PROBS_WINDOW_STACKP 16384U |
Option flag to activate callback triggers for stacking probabilities. More... | |
#define | VRNA_PROBS_WINDOW_UP_SPLIT 32768U |
Option flag to activate callback triggers for unpaired probabilities (split up into different loop types) More... | |
Functions | |
vrna_ep_t * | vrna_pfl_fold (const char *sequence, int window_size, int max_bp_span, float cutoff) |
Compute base pair probabilities using a sliding-window approach. More... | |
void | vrna_pfl_fold_cb (const char *sequence, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data) |
Compute base pair probabilities using a sliding-window approach (callback version) More... | |
double ** | vrna_pfl_fold_up (const char *sequence, int ulength, int window_size, int max_bp_span) |
Compute probability of contiguous unpaired segments. More... | |
void | vrna_pfl_fold_up_cb (const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data) |
Compute probability of contiguous unpaired segments. More... | |
void | vrna_probs_window (vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_callback *cb, void *data) |
Compute various equilibrium probabilities under a sliding window approach. More... | |
void | update_pf_paramsLP (int length) |
vrna_ep_t * | pfl_fold (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup) |
Compute partition functions for locally stable secondary structures. More... | |
vrna_ep_t * | pfl_fold_par (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters) |
Compute partition functions for locally stable secondary structures. | |
void | putoutpU_prob (double **pU, int length, int ulength, FILE *fp, int energies) |
Writes the unpaired probabilities (pU) or opening energies into a file. More... | |
void | putoutpU_prob_bin (double **pU, int length, int ulength, FILE *fp, int energies) |
Writes the unpaired probabilities (pU) or opening energies into a binary file. More... | |
#define VRNA_PROBS_WINDOW_BPP 4096U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for pairing probabilities.
#define VRNA_PROBS_WINDOW_UP 8192U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for unpaired probabilities.
#define VRNA_PROBS_WINDOW_STACKP 16384U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for stacking probabilities.
#define VRNA_PROBS_WINDOW_UP_SPLIT 32768U |
#include <ViennaRNA/LPfold.h>
Option flag to activate callback triggers for unpaired probabilities (split up into different loop types)
vrna_ep_t* vrna_pfl_fold | ( | const char * | sequence, |
int | window_size, | ||
int | max_bp_span, | ||
float | cutoff | ||
) |
#include <ViennaRNA/LPfold.h>
Compute base pair probabilities using a sliding-window approach.
This is a simplified wrapper to vrna_probs_window() that given a nucleid acid sequence, a window size, a maximum base pair span, and a cutoff value computes the pair probabilities for any base pair in any window. The pair probabilities are returned as a list and the user has to take care to free() the memory occupied by the list.
sequence | The nucleic acid input sequence |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
cutoff | A cutoff value that omits all pairs with lower probability |
void vrna_pfl_fold_cb | ( | const char * | sequence, |
int | window_size, | ||
int | max_bp_span, | ||
vrna_probs_window_callback * | cb, | ||
void * | data | ||
) |
#include <ViennaRNA/LPfold.h>
Compute base pair probabilities using a sliding-window approach (callback version)
This is a simplified wrapper to vrna_probs_window() that given a nucleid acid sequence, a window size, a maximum base pair span, and a cutoff value computes the pair probabilities for any base pair in any window. It is similar to vrna_pfl_fold() but uses a callback mechanism to return the pair probabilities.
Read the details for vrna_probs_window() for details on the callback implementation!
sequence | The nucleic acid input sequence |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
cb | The callback function which collects the pair probability data for further processing |
data | Some arbitrary data structure that is passed to the callback cb |
double** vrna_pfl_fold_up | ( | const char * | sequence, |
int | ulength, | ||
int | window_size, | ||
int | max_bp_span | ||
) |
#include <ViennaRNA/LPfold.h>
Compute probability of contiguous unpaired segments.
This is a simplified wrapper to vrna_probs_window() that given a nucleic acid sequence, a maximum length of unpaired segments (ulength
), a window size, and a maximum base pair span computes the equilibrium probability of any segment not exceeding ulength
. The probabilities to be unpaired are returned as a 1-based, 2-dimensional matrix with dimensions , where
is the length of the sequence and
is the maximum segment length. As an example, the probability of a segment of size 5 starting at position 100 is stored in the matrix entry
.
It is the users responsibility to free the memory occupied by this matrix.
sequence | The nucleic acid input sequence |
ulength | The maximal length of an unpaired segment |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
ulength
void vrna_pfl_fold_up_cb | ( | const char * | sequence, |
int | ulength, | ||
int | window_size, | ||
int | max_bp_span, | ||
vrna_probs_window_callback * | cb, | ||
void * | data | ||
) |
#include <ViennaRNA/LPfold.h>
Compute probability of contiguous unpaired segments.
This is a simplified wrapper to vrna_probs_window() that given a nucleic acid sequence, a maximum length of unpaired segments (ulength
), a window size, and a maximum base pair span computes the equilibrium probability of any segment not exceeding ulength
. It is similar to vrna_pfl_fold_up() but uses a callback mechanism to return the unpaired probabilities.
Read the details for vrna_probs_window() for details on the callback implementation!
sequence | The nucleic acid input sequence |
ulength | The maximal length of an unpaired segment |
window_size | The size of the sliding window |
max_bp_span | The maximum distance along the backbone between two nucleotides that form a base pairs |
cb | The callback function which collects the pair probability data for further processing |
data | Some arbitrary data structure that is passed to the callback cb |
ulength
void vrna_probs_window | ( | vrna_fold_compound_t * | fc, |
int | ulength, | ||
unsigned int | options, | ||
vrna_probs_window_callback * | cb, | ||
void * | data | ||
) |
#include <ViennaRNA/LPfold.h>
Compute various equilibrium probabilities under a sliding window approach.
fc | The fold compound with sequence data, model settings and precomputed energy parameters |
ulength | The maximal length of an unpaired segment (only for unpaired probability computations) |
cb | The callback function which collects the pair probability data for further processing |
data | Some arbitrary data structure that is passed to the callback cb |
options | Option flags to control the behavior of this function |
void update_pf_paramsLP | ( | int | length | ) |
#include <ViennaRNA/LPfold.h>
length |
vrna_ep_t* pfl_fold | ( | char * | sequence, |
int | winSize, | ||
int | pairSize, | ||
float | cutoffb, | ||
double ** | pU, | ||
vrna_ep_t ** | dpp2, | ||
FILE * | pUfp, | ||
FILE * | spup | ||
) |
#include <ViennaRNA/LPfold.h>
Compute partition functions for locally stable secondary structures.
pfl_fold computes partition functions for every window of size 'winSize' possible in a RNA molecule, allowing only pairs with a span smaller than 'pairSize'. It returns the mean pair probabilities averaged over all windows containing the pair in 'pl'. 'winSize' should always be >= 'pairSize'. Note that in contrast to Lfold(), bases outside of the window do not influence the structure at all. Only probabilities higher than 'cutoffb' are kept.
If 'pU' is supplied (i.e is not the NULL pointer), pfl_fold() will also compute the mean probability that regions of length 'u' and smaller are unpaired. The parameter 'u' is supplied in 'pup[0][0]'. On return the 'pup' array will contain these probabilities, with the entry on 'pup[x][y]' containing the mean probability that x and the y-1 preceding bases are unpaired. The 'pU' array needs to be large enough to hold n+1 float* entries, where n is the sequence length.
If an array dpp2 is supplied, the probability of base pair (i,j) given that there already exists a base pair (i+1,j-1) is also computed and saved in this array. If pUfp is given (i.e. not NULL), pU is not saved but put out imediately. If spup is given (i.e. is not NULL), the pair probabilities in pl are not saved but put out imediately.
sequence | RNA sequence |
winSize | size of the window |
pairSize | maximum size of base pair |
cutoffb | cutoffb for base pairs |
pU | array holding all unpaired probabilities |
dpp2 | array of dependent pair probabilities |
pUfp | file pointer for pU |
spup | file pointer for pair probabilities |
void putoutpU_prob | ( | double ** | pU, |
int | length, | ||
int | ulength, | ||
FILE * | fp, | ||
int | energies | ||
) |
#include <ViennaRNA/LPfold.h>
Writes the unpaired probabilities (pU) or opening energies into a file.
Can write either the unpaired probabilities (accessibilities) pU or the opening energies -log(pU)kT into a file
pU | pair probabilities |
length | length of RNA sequence |
ulength | maximum length of unpaired stretch |
fp | file pointer of destination file |
energies | switch to put out as opening energies |
void putoutpU_prob_bin | ( | double ** | pU, |
int | length, | ||
int | ulength, | ||
FILE * | fp, | ||
int | energies | ||
) |
#include <ViennaRNA/LPfold.h>
Writes the unpaired probabilities (pU) or opening energies into a binary file.
Can write either the unpaired probabilities (accessibilities) pU or the opening energies -log(pU)kT into a file
pU | pair probabilities |
length | length of RNA sequence |
ulength | maximum length of unpaired stretch |
fp | file pointer of destination file |
energies | switch to put out as opening energies |