Tree Representation of Secondary Structures

Defines

VRNA_STRUCTURE_TREE_HIT

#include <ViennaRNA/utils/structures.h>

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

See also

vrna_db_to_tree_string()

VRNA_STRUCTURE_TREE_SHAPIRO_SHORT

#include <ViennaRNA/utils/structures.h>

(short) Coarse Grained representation of a secondary structure

See also

vrna_db_to_tree_string()

VRNA_STRUCTURE_TREE_SHAPIRO

#include <ViennaRNA/utils/structures.h>

(full) Coarse Grained representation of a secondary structure

See also

vrna_db_to_tree_string()

VRNA_STRUCTURE_TREE_SHAPIRO_EXT

#include <ViennaRNA/utils/structures.h>

(extended) Coarse Grained representation of a secondary structure

See also

vrna_db_to_tree_string()

VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT

#include <ViennaRNA/utils/structures.h>

(weighted) Coarse Grained representation of a secondary structure

See also

vrna_db_to_tree_string()

VRNA_STRUCTURE_TREE_EXPANDED

#include <ViennaRNA/utils/structures.h>

Expanded Tree representation of a secondary structure.

See also

vrna_db_to_tree_string()

Functions

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] )
VRNA_STRUCTURE_TREE_SHAPIRO_SHORT - (short) Coarse Grained representation of a secondary structure (same as Shapiro [1988] , 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] )
VRNA_STRUCTURE_TREE_SHAPIRO_EXT - (extended) Coarse Grained representation of a secondary structure (same as Shapiro [1988] , 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

sec_structure_representations_tree

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 [1988]

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.

See also

vrna_db_to_tree_string(), VRNA_STRUCTURE_TREE_EXPANDED, VRNA_STRUCTURE_TREE_HIT, sec_structure_representations_tree

Warning

This function only accepts Expanded and HIT tree representations!

Parameters:

tree – A linear tree string representation of a secondary structure

Returns:

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