Partition functions for locally stable secondary structures
RNA Secondary Structure Prediction » Predicting Locally stable structures of large sequences RNA Secondary Structure Prediction » | Computing Partition Functions and Pair Probabilities
Collaboration diagram for Partition functions for locally stable secondary structures:

## Files

file | LPfold.h
| Function declarations of partition function variants of the Lfold algorithm.

## Functions

void | update_pf_paramsLP (int length)
plist * | pfl_fold (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, plist **dpp2, FILE *pUfp, FILE *spup)
| Compute partition functions for locally stable secondary structures. More...
plist * | pfl_fold_par (char *sequence, int winSize, int pairSize, float cutoffb, double **pU, plist **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...

## Detailed Description

## Function Documentation

void update_pf_paramsLP | ( | int | length | ) |

`#include <ViennaRNA/LPfold.h>`

Parameters

  length |

plist* pfl_fold | ( | char * | sequence,
|  | int | winSize,
|  | int | pairSize,
|  | float | cutoffb,
|  | double ** | pU,
|  | plist ** | 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.

Parameters

  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

Returns
  list of 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

Parameters

  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

Parameters

  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