base_pairs_from_dot_bracket#

biotite.structure.base_pairs_from_dot_bracket(dot_bracket_notation)[source]#

Extract the base pairs from a nucleic-acid-strand in dot-bracket-letter-notation (DBL-notation). [1]

The nucleic acid strand is represented as nucleotide sequence, where the nucleotides are counted continiously from zero.

Parameters:
dot_bracket_notationstr

The DBL-notation.

Returns:
basepairsndarray, shape=(n,2)

Each row corresponds to the positions of the bases in the sequence.

See also

dot_bracket

References

Examples

The notation string '(..).' contains a base pair between the indices 0 and 3. This pairing interaction can be extracted conveniently by the use of base_pairs_from_dot_bracket():

>>> base_pairs_from_dot_bracket('(..).')
array([[0, 3]])