Detailed Description

Secondary structures can be readily represented as trees, where internal nodes represent base pairs, and leaves represent unpaired nucleotides. The dot-bracket structure string already is a tree represented by a string of parenthesis (base pairs) and dots for the leaf nodes (unpaired nucleotides).

See Tree Representations of Secondary Structures for a detailed description on tree representation of secondary structures.

Collaboration diagram for Tree Representation of Secondary Structures:

Macros
#define	VRNA_STRUCTURE_TREE_HIT 1U
	Homeomorphically Irreducible Tree (HIT) representation of a secondary structure. More...

#define	VRNA_STRUCTURE_TREE_SHAPIRO_SHORT 2U
	(short) Coarse Grained representation of a secondary structure More...

#define	VRNA_STRUCTURE_TREE_SHAPIRO 3U
	(full) Coarse Grained representation of a secondary structure More...

#define	VRNA_STRUCTURE_TREE_SHAPIRO_EXT 4U
	(extended) Coarse Grained representation of a secondary structure More...

#define	VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT 5U
	(weighted) Coarse Grained representation of a secondary structure More...

#define	VRNA_STRUCTURE_TREE_EXPANDED 6U
	Expanded Tree representation of a secondary structure. More...

Functions
char *	vrna_db_to_tree_string (const char *structure, unsigned int type)
	Convert a Dot-Bracket structure string into tree string representation. More...

char *	vrna_tree_string_unweight (const char *structure)
	Remove weights from a linear string tree representation of a secondary structure. More...

char *	vrna_tree_string_to_db (const char *tree)
	Convert a linear tree string representation of a secondary structure back to Dot-Bracket notation. More...

Macro Definition Documentation

#define VRNA_STRUCTURE_TREE_HIT 1U

#include <ViennaRNA/utils/structures.h>

Homeomorphically Irreducible Tree (HIT) representation of a secondary structure.

See also: vrna_db_to_tree_string()

#define VRNA_STRUCTURE_TREE_SHAPIRO_SHORT 2U

#include <ViennaRNA/utils/structures.h>

(short) Coarse Grained representation of a secondary structure

See also: vrna_db_to_tree_string()

#define VRNA_STRUCTURE_TREE_SHAPIRO 3U

#include <ViennaRNA/utils/structures.h>

(full) Coarse Grained representation of a secondary structure

See also: vrna_db_to_tree_string()

#define VRNA_STRUCTURE_TREE_SHAPIRO_EXT 4U

#include <ViennaRNA/utils/structures.h>

(extended) Coarse Grained representation of a secondary structure

See also: vrna_db_to_tree_string()

#define VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT 5U

#include <ViennaRNA/utils/structures.h>

(weighted) Coarse Grained representation of a secondary structure

See also: vrna_db_to_tree_string()

#define VRNA_STRUCTURE_TREE_EXPANDED 6U

#include <ViennaRNA/utils/structures.h>

Expanded Tree representation of a secondary structure.

See also: vrna_db_to_tree_string()

Function Documentation

char* vrna_db_to_tree_string	(	const char *	structure,
		unsigned int	type
	)

#include <ViennaRNA/utils/structures.h>

Convert a Dot-Bracket structure string into tree string representation.

This function allows one to convert a secondary structure in dot-bracket notation into one of the various tree representations for secondary structures. The resulting tree is then represented as a string of parenthesis and node symbols, similar to to the Newick format.

Currently we support conversion into the following formats, denoted by the value of parameter type:

VRNA_STRUCTURE_TREE_HIT - Homeomorphically Irreducible Tree (HIT) representation of a secondary structure. (See also Fontana et al. 1993 [8])
VRNA_STRUCTURE_TREE_SHAPIRO_SHORT - (short) Coarse Grained representation of a secondary structure (same as Shapiro 1988 [21], but with root node R and without S nodes for the stems)
VRNA_STRUCTURE_TREE_SHAPIRO - (full) Coarse Grained representation of a secondary structure (See also Shapiro 1988 [21])
VRNA_STRUCTURE_TREE_SHAPIRO_EXT - (extended) Coarse Grained representation of a secondary structure (same as Shapiro 1988 [21], but external nodes denoted as E )
VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT - (weighted) Coarse Grained representation of a secondary structure (same as VRNA_STRUCTURE_TREE_SHAPIRO_EXT but with additional weights for number of unpaired nucleotides in loop, and number of pairs in stems)
VRNA_STRUCTURE_TREE_EXPANDED - Expanded Tree representation of a secondary structure.

See also: Tree Representations of Secondary Structures

Parameters

structure	The null-terminated dot-bracket structure string
type	A switch to determine the type of tree string representation

Returns: A tree representation of the input structure

char* vrna_tree_string_unweight ( const char * structure )

#include <ViennaRNA/utils/structures.h>

Remove weights from a linear string tree representation of a secondary structure.

This function strips the weights of a linear string tree representation such as HIT, or Coarse Grained Tree sensu Shapiro [21]

See also: vrna_db_to_tree_string()

Parameters

structure A linear string tree representation of a secondary structure with weights

Returns: A linear string tree representation of a secondary structure without weights

char* vrna_tree_string_to_db ( const char * tree )

#include <ViennaRNA/utils/structures.h>

Convert a linear tree string representation of a secondary structure back to Dot-Bracket notation.

Warning: This function only accepts Expanded and HIT tree representations!

See also: vrna_db_to_tree_string(), VRNA_STRUCTURE_TREE_EXPANDED, VRNA_STRUCTURE_TREE_HIT, Tree Representations of Secondary Structures

Parameters

tree	A linear tree string representation of a secondary structure

Returns: A dot-bracket notation of the secondary structure provided in tree

Detailed Description

Macros

Functions

Macro Definition Documentation

Function Documentation