H/inverse.h File Reference

Inverse folding routines. More...

Functions
float	inverse_fold (char start, const char target)
	Find sequences with predefined structure.
float	inverse_pf_fold (char start, const char target)
	Find sequence that maximizes probability of a predefined structure.
Variables
char *	symbolset
	This global variable points to the allowed bases, initially "AUGC".
float	final_cost
	when to stop inverse_pf_fold()
int	give_up
	default 0: try to minimize structure distance even if no exact solution can be found
int	inv_verbose
	print out substructure on which inverse_fold() fails

Detailed Description

Inverse folding routines.

Function Documentation

float inverse_fold	(	char *	start,
		const char *	target
	)

Find sequences with predefined structure.

This function searches for a sequence with minimum free energy structure provided in the parameter 'target', starting with sequence 'start'. It returns 0 if the search was successful, otherwise a structure distance in terms of the energy difference between the search result and the actual target 'target' is returned. The found sequence is returned in 'start'. If give_up is set to 1, the function will return as soon as it is clear that the search will be unsuccessful, this speeds up the algorithm if you are only interested in exact solutions.

Parameters:

	start	The start sequence
	target	The target secondary structure in dot-bracket notation

Returns:: The distance to the target in case a search was unsuccessful, 0 otherwise

float inverse_pf_fold	(	char *	start,
		const char *	target
	)

Find sequence that maximizes probability of a predefined structure.

This function searches for a sequence with maximum probability to fold into the provided structure 'target' using the partition function algorithm. It returns $-kT \cdot \log(p)$ where $p$ is the frequency of 'target' in the ensemble of possible structures. This is usually much slower than inverse_fold().

Parameters:

	start	The start sequence
	target	The target secondary structure in dot-bracket notation

Returns:: The distance to the target in case a search was unsuccessful, 0 otherwise

Variable Documentation

char* symbolset

This global variable points to the allowed bases, initially "AUGC".

It can be used to design sequences from reduced alphabets.

H/inverse.h File Reference

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation