Suboptimal structures sensu Stiegler et al. 1984 / Zuker et al. 1989

Overview

// global functions

vrna_subopt_solution_t* vrna_subopt_zuker (vrna_fold_compound_t* vc)
SOLUTION* zukersubopt (const char* string)

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

Detailed Documentation

Global Functions

vrna_subopt_solution_t* vrna_subopt_zuker (vrna_fold_compound_t* vc)
Compute Zuker type suboptimal structures.

Compute Suboptimal structures according to M. Zuker [24] , 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.

Bug Due to resizing, any pre-existing constraints will be lost!

SWIG Wrapper Notes This function is attached as method subopt_zuker() to objects of type fold_compound

Parameters:

vc fold compound

Returns:

List of zuker suboptimal structures

Note

This function internally uses the cofold implementation to compute the suboptimal structures. For that purpose, the function doubles the sequence and enlarges the DP matrices, which in fact will grow by a factor of 4 during the computation! At the end of the structure prediction, everything will be re-set to its original requriements, i.e. normal sequence, normal (empty) DP matrices.

SOLUTION* zukersubopt (const char* string)
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
    )
Compute Zuker type suboptimal structures.
Deprecated use vrna_zukersubopt() instead