biotite.structure.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,) (default: None)
The score for each base pair, which is passed on to
pseudoknots()
- max_pseudoknot_orderint (default: None)
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()
.
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 sequence
ACGTC
has a length of 5. If there was to be a pairing interaction between theA
andT
, 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] '(..).'