# Pseudoknots

Implementations to predict pseudoknotted structures.

  Typedefs

  typedef int (*vrna_pk_plex_score_f)(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().

    See also

    vrna_pk_plex_opt_fun(), vrna_pk_plex()

    Param pt:

      The secondary structure (without pseudoknot) in pair table notation

    Param start_5:

      The start coordinate of the 5’ site of the pseudoknot interaction

    Param end_5:

      The end coordinate of the 5’ site of the pseudoknot interaction

    Param start_3:

      The start coordinate of the 3’ site of the pseudoknot interaction

    Param end_3:

      The end coordinate of the 3’ site of the pseudoknot interaction

    Param data:

      An arbitrary data structure passed from the calling function

    Return:

      The energy (penalty) of the resulting pseudoknot

  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>
  typedef struct vrna_pk_plex_option_s *vrna_pk_plex_opt_t
    #include <ViennaRNA/pk_plex.h>

    RNA PKplex options object.

    See also

    vrna_pk_plex_opt_defaults(), vrna_pk_plex_opt(), vrna_pk_plex_opt_fun(), vrna_pk_plex(), vrna_pk_plex_score_f

  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.

    See also

    #vrna_pk_plex_results_s, vrna_pk_plex()

  Functions

  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_pk_plex_score_f 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.

    Parameters:

      - 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

    Returns:

      A list of potentially pseudoknotted structures (Last element in the list indicated by NULL value in vrna_pk_plex_result_s.structure)

  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.

    See also

    vrna_pk_plex()

    Parameters:

      - sequence – The RNA sequence

      - unpaired – The maximum number of unpaired nucleotides, i.e. length of interaction

      - cutoff – A cutoff value for unpaired probabilities

    Returns:

      Opening energies as required for vrna_pk_plex()

  vrna_pk_plex_opt_t vrna_pk_plex_opt_defaults(void)
    #include <ViennaRNA/pk_plex.h>

    Default options for PKplex algorithm.

    See also

    vrna_pk_plex(), vrna_pk_plex_opt(), vrna_pk_plex_opt_fun()

    Returns:

      An options data structure suitabe for PKplex computations

  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.

    See also

    vrna_pk_plex(), vrna_pk_plex_opt_defaults(), vrna_pk_plex_opt_fun()

    Parameters:

      - 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

    Returns:

      An options data structure suitabe for PKplex computations

  vrna_pk_plex_opt_t vrna_pk_plex_opt_fun(unsigned int delta, unsigned int max_interaction_length, vrna_pk_plex_score_f scoring_function, void *scoring_data)
    #include <ViennaRNA/pk_plex.h>

    Simple options for PKplex algorithm.

    See also

    vrna_pk_plex(), vrna_pk_plex_opt_defaults(), vrna_pk_plex_opt(), vrna_pk_plex_score_f

    Parameters:

      - 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)

    Returns:

      An options data structure suitabe for PKplex computations

  struct vrna_pk_plex_result_s
    #include <ViennaRNA/pk_plex.h>

    A result of the RNA PKplex interaction prediction.

    See also

    vrna_pk_plex_t

    Public Members

    char *structure

      Secondary Structure in dot-bracket notation.

    double energy

      Net free energy in kcal/mol.

    double dGpk

      Free energy of PK loop in kcal/mol.

    double dGint

      Free energy of PK forming duplex interaction.

    double dG1

      Opening energy for the 5’ interaction site used in the heuristic.

    double dG2

      Opening energy for the 3’ interaction site used in the heuristic.

    unsigned int start_5

      Start coordinate of the 5’ interaction site.

    unsigned int end_5

      End coordinate of the 5’ interaction site.

    unsigned int start_3

      Start coordinate of the 3’ interaction site.

    unsigned int end_3

      End coordinate of the 3’ interaction site.