DuplexApp

class biotite.application_v2.viennarna.DuplexApp(path: PathLike[str] | str = 'RNAduplex')

Bases: LocalApp

A handle to ViennaRNA’s RNAduplex software.

Parameters:

pathstr, optional

Path of the RNAduplex binary.

Examples

>>> result = DuplexApp().run(
...     NucleotideSequence("AAAAGGGGGGG"), NucleotideSequence("CCCCCCCAAAA")
... ).result()
>>> print(result.dot_bracket)
.(((((((&))))))).
>>> print(result.free_energy)
-17.2
>>> print(result.spans)
[(3, 11), (0, 8)]
>>> print(result.base_pairs())
[[ 0  4  1  6]
 [ 0  5  1  5]
 [ 0  6  1  4]
 [ 0  7  1  3]
 [ 0  8  1  2]
 [ 0  9  1  1]
 [ 0 10  1  0]]

run(sequence1: NucleotideSequence, sequence2: NucleotideSequence, temperature: float = 37, **kwargs: Any) → CommandSetup[CofoldedRNA]

Predict the hybridization structure of two strands.

Parameters:

sequence1, sequence2NucleotideSequence

The two RNA strands.

temperaturefloat, optional

The temperature (°C) to be assumed for the energy parameters.

**kwargs

Additional command line options.

Returns:

futureFuture of CofoldedRNA

A handle to the running computation. Only the interacting parts of the strands are covered by the structure, as given by CofoldedRNA.spans.