Suboptimal Structures sensu Zuker

The algorithm to compute optimal secondary structures that contain a particular base pair has been published by Zuker [1989] and is based on ideas for predicting structures for circular RNAs, in particular viroids, as presented in Steger et al. [1984].

Functions

SOLUTION *zukersubopt(const char *string)

#include <ViennaRNA/subopt.h>

Compute Zuker type suboptimal structures.

Compute Suboptimal structures according to M. Zuker, i.e. for every possible base pair the minimum energy structure containing the resp. base pair. Returns a list of these structures and their energies.

Deprecated:: use vrna_zukersubopt() instead

Parameters:

string – RNA sequence

Returns:

List of zuker suboptimal structures

SOLUTION *zukersubopt_par(const char *string, vrna_param_t *parameters)

#include <ViennaRNA/subopt.h>

Compute Zuker type suboptimal structures.

Deprecated:: use vrna_zukersubopt() instead

vrna_subopt_solution_t *vrna_subopt_zuker(vrna_fold_compound_t *fc)

#include <ViennaRNA/subopt_zuker.h>

Compute Zuker type suboptimal structures.

Compute Suboptimal structures according to Zuker [1989] , i.e. for every possible base pair the minimum energy structure containing the resp. base pair. Returns a list of these structures and their energies.

SWIG Wrapper Notes:: This function is attached as method subopt_zuker() to objects of type fold_compound. See, e.g. RNA.fold_compound.subopt_zuker() in the Python API.