biotite.structure.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
- 1
M. Antczak, M. Popenda, T. Zok, M. Zurkowski, R. W. Adamiak, M. Szachniuk, “New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation,” Bioinformatics, vol. 34, pp. 1304–1312, April 2018. doi: 10.1093/bioinformatics/btx783
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]])