`dot_bracket`#

biotite.structure.dot_bracket(basepairs, length, scores=None, max_pseudoknot_order=None)[source]#

Represent 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:

basepairsndarray, shape=(n,2): Each row corresponds to the positions of the bases in the strand.
lengthint: The number of bases in the strand.
scoresndarray, dtype=int, shape=(n,): The score for each base pair, which is passed on to pseudoknots().
max_pseudoknot_orderint: The maximum pseudoknot order to be found. If a base pair would be of a higher order, it is represented as unpaired. If None is given, all pseudoknot orders are evaluated.

Returns:

notationslist [str, …]: The DBL-notation for each solution from pseudoknots().

See also

base_pairs_from_dot_bracket: The reverse operation.
dot_bracket_from_structure: Compute the dot bracket notation from a structure.
base_pairs: Compute the base pairs from a structure as passed to this function.
pseudoknots: Get the pseudoknot order for each base pair.

References

Examples

The sequence ACGTC has a length of 5. If there was to be a pairing interaction between the A and T, basepairs would have the form:

>>> import numpy as np
>>> basepairs = np.array([[0, 3]])

The DBL Notation can then be found with dot_bracket():

>>> dot_bracket(basepairs, 5)[0]
'(..).'

dot_bracket#