Pair Table Representation of Secondary Structures

Functions

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.

SWIG Wrapper Notes:

This functions is wrapped as overloaded function ptable() that takes an optional argument options to specify which type of matching brackets should be considered during conversion. The default set is round brackets, i.e. VRNA_BRACKETS_RND. See, e.g. RNA.ptable() in the Python API.

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 *structure, 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 or dot-bracket-ext-notation, and converts it into a pair table representation.

SWIG Wrapper Notes:

This functions is wrapped as overloaded function ptable() that takes an optional argument options to specify which type of matching brackets should be considered during conversion. The default set is round brackets, i.e. VRNA_BRACKETS_RND. See, e.g. RNA.ptable() in the Python API.

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

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.

Parameters:

  • structure – Secondary structure in dot-bracket-ext-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_BRACKETS_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_ali_get(const char *structure)
#include <ViennaRNA/utils/structures.h>

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

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