Pair Table Representation of Secondary Structures

Detailed Description

Collaboration diagram for Pair Table Representation of Secondary Structures:

Functions
short *	vrna_ptable (const char *structure)
	Create a pair table from a dot-bracket notation of a secondary structure. More...
short *	vrna_ptable_from_string (const char *string, unsigned int options)
	Create a pair table for a secondary structure string. More...
short *	vrna_pt_pk_get (const char *structure)
	Create a pair table of a secondary structure (pseudo-knot version) More...
short *	vrna_ptable_copy (const short *pt)
	Get an exact copy of a pair table. More...
short *	vrna_pt_ali_get (const char *structure)
	Create a pair table of a secondary structure (snoop align version)
short *	vrna_pt_snoop_get (const char *structure)
	Create a pair table of a secondary structure (snoop version) More...
short *	vrna_pt_pk_remove (const short *ptable, unsigned int options)
	Remove pseudo-knots from a pair table. More...

Function Documentation

short* vrna_ptable

(

const char *

structure

)

#include <ViennaRNA/utils/structures.h>

Create a pair table from a dot-bracket notation of a secondary structure.

Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.

See also

vrna_ptable_from_string(), vrna_db_from_ptable()

Parameters

structure

The secondary structure in dot-bracket notation

Returns

A pointer to the created pair_table

short* vrna_ptable_from_string	(	const char *	string,
		unsigned int	options
	)

#include <ViennaRNA/utils/structures.h>

Create a pair table for a secondary structure string.

This function takes an input string of a secondary structure annotation in Dot-Bracket Notation (a.k.a. Dot-Parenthesis Notation) or Extended Dot-Bracket Notation, and converts it into a pair table representation.

Note

This function also extracts crossing base pairs, i.e. pseudo-knots if more than a single matching bracket type is allowed through the bitmask options.

See also

vrna_ptable(), vrna_db_from_ptable(), vrna_db_flatten_to(), vrna_pt_pk_remove() VRNA_BRACKETS_RND, VRNA_BRACKETS_ANG, VRNA_BRACKETS_CLY, VRNA_BRACKETS_SQR, VRNA_BRACKETS_ALPHA, VRNA_BRACKETS_DEFAULT, VRNA_BRACKETS_ANY

Parameters

string	Secondary structure in Extended Dot-Bracket Notation
options	A bitmask to specify which brackets are recognized during conversion to pair table

Returns

A pointer to a new pair table of the provided secondary structure

short* vrna_pt_pk_get

(

const char *

structure

)

#include <ViennaRNA/utils/structures.h>

Create a pair table of a secondary structure (pseudo-knot version)

Returns a newly allocated table, such that table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure.

In contrast to vrna_ptable() this function also recognizes the base pairs denoted by '[' and ']' brackets. Thus, this function behaves like

vrna_ptable_from_string(structure, #VRNA_BRACKET_RND | VRNA_BRACKETS_SQR)

See also

vrna_ptable_from_string()

Parameters

structure

The secondary structure in (extended) dot-bracket notation

Returns

A pointer to the created pair_table

short* vrna_ptable_copy

(

const short *

pt

)

#include <ViennaRNA/utils/structures.h>

Get an exact copy of a pair table.

Parameters

pt	The pair table to be copied

Returns

A pointer to the copy of 'pt'

short* vrna_pt_snoop_get

(

const char *

structure

)

#include <ViennaRNA/utils/structures.h>

Create a pair table of a secondary structure (snoop version)

returns a newly allocated table, such that: table[i]=j if (i.j) pair or 0 if i is unpaired, table[0] contains the length of the structure. The special pseudoknotted H/ACA-mRNA structure is taken into account.

short* vrna_pt_pk_remove	(	const short *	ptable,
		unsigned int	options
	)

#include <ViennaRNA/utils/structures.h>

Remove pseudo-knots from a pair table.

This function removes pseudo-knots from an input structure by determining the minimum number of base pairs that need to be removed to make the structure pseudo-knot free.

To accomplish that, we use a dynamic programming algorithm similar to the Nussinov maxmimum matching approach.

See also

vrna_db_pk_remove()

Parameters

ptable	Input structure that may include pseudo-knots
options

Returns

The input structure devoid of pseudo-knots