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