biotite.structure.base_pairs_from_dot_bracket

biotite.structure.base_pairs_from_dot_bracket(dot_bracket_notation)

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

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 of base_pairs_from_dot_bracket():

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