`AliduplexApp`#

class biotite.application_v2.viennarna.AliduplexApp(path: PathLike[str] | str = 'RNAaliduplex')[source]#

Bases: LocalApp

A handle to ViennaRNA’s RNAaliduplex software.

Parameters:

pathstr, optional: Path of the RNAaliduplex binary.

Examples

>>> matrix = SubstitutionMatrix.std_nucleotide_matrix()
>>> alignment1 = align_multiple(
...     [
...         NucleotideSequence("AAAAGGGGGGG"),
...         NucleotideSequence("AAACGGGGGGG"),
...         NucleotideSequence("AAAAAGGGGGGG"),
...         NucleotideSequence("AACGGGGGGG"),
...     ],
...     matrix,
...     terminal_penalty=False,
... )[0]
>>> print(alignment1)
-AAAAGGGGGGG
-AAACGGGGGGG
AAAAAGGGGGGG
--AACGGGGGGG
>>> alignment2 = align_multiple(
...     [
...         NucleotideSequence("CCCCCCCAAAA"),
...         NucleotideSequence("CCCCCCGAAAA"),
...         NucleotideSequence("CCCCCCCAAA"),
...         NucleotideSequence("CCCCCCCAAAAA"),
...     ],
...     matrix,
...     terminal_penalty=False,
... )[0]
>>> print(alignment2)
CCCCCCCAAAA-
CCCCCCGAAAA-
CCCCCCCAAA--
CCCCCCCAAAAA
>>> result = AliduplexApp().run(alignment1, alignment2).result()
>>> print(result.dot_bracket)
.(((((((&))))))).
>>> print(result.free_energy)
-16.17
>>> print(result.base_pairs())
[[ 0  5  1  6]
 [ 0  6  1  5]
 [ 0  7  1  4]
 [ 0  8  1  3]
 [ 0  9  1  2]
 [ 0 10  1  1]
 [ 0 11  1  0]]
>>> print(result.base_pairs_of(0))
[[ 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(alignment1: Alignment, alignment2: Alignment, temperature: float = 37, **kwargs: Any) → CommandSetup[CofoldedAlignment]#

Predict the hybridization structure of two alignments.

Parameters:

alignment1, alignment2Alignment: The two RNA alignments.
temperaturefloat, optional: The temperature (°C) to be assumed for the energy parameters.
**kwargs: Additional command line options.

Returns:

futureFuture of CofoldedAlignment: A handle to the running computation.

Notes

Unlike AlifoldApp, RNAaliduplex does not report the covariance contribution separately. Therefore CofoldedAlignment.free_energy contains the total energy, i.e. the sum of the physical free energy and the covariance term, and CofoldedAlignment.covariance_energy is None.

AliduplexApp#

`AliduplexApp`#