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

Detailed Description

Collaboration diagram for Suboptimal Structures sensu Stiegler et al. 1984 / Zuker et al. 1989:

Functions
vrna_subopt_solution_t *	vrna_subopt_zuker (vrna_fold_compound_t *vc)
	Compute Zuker type suboptimal structures. More...
SOLUTION *	zukersubopt (const char *string)
	Compute Zuker type suboptimal structures. More...
SOLUTION *	zukersubopt_par (const char *string, vrna_param_t *parameters)
	Compute Zuker type suboptimal structures. More...

Function Documentation

vrna_subopt_solution_t * vrna_subopt_zuker

(

vrna_fold_compound_t *

vc

)

#include <ViennaRNA/subopt.h>

Compute Zuker type suboptimal structures.

Compute Suboptimal structures according to M. Zuker [27] , 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.

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.

Bug:

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

See also

vrna_subopt(), zukersubopt(), zukersubopt_par()

Parameters

vc	fold compound

Returns

List of zuker suboptimal structures

SWIG Wrapper Notes:

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

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