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.. _genetic-codes:
Using genetic codes
^^^^^^^^^^^^^^^^^^^
Selecting codes in methods that support them
""""""""""""""""""""""""""""""""""""""""""""
In cases where a ``cogent3`` object method has a ``gc`` argument, you can just use the number under "Code ID" column.
For example, I've created a partial codon in ``"s1"``
.. jupyter-execute::
from cogent3 import make_aligned_seqs
data = {
"s1": "GCTCATGCCAGCTCTTTACAGCATGAGAACA--AGT",
"s2": "ACTCATGCCAACTCATTACAGCATGAGAACAGCAGT",
"s3": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT",
"s4": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT",
"s5": "ACTCATGCCAGCTCAGTACAGCATGAGAACAGCAGT",
}
nt_seqs = make_aligned_seqs(data=data, moltype="dna")
nt_seqs
We specify the genetic code, and we allow incomplete codons. In this case, if a codon contains a gap, they are converted to ``?`` in the translation.
.. jupyter-execute::
nt_seqs.get_translation(gc=1, incomplete_ok=True)
Translate DNA sequences
"""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code
standard_code = get_code(1)
standard_code.translate("TTTGCAAAC")
Conversion to a ``ProteinSequence`` from a ``DnaSequence`` is shown in :ref:`translation`.
Translate all six frames
""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code, make_seq
standard_code = get_code(1)
seq = make_seq("ATGCTAACATAAA", moltype="dna")
translations = standard_code.sixframes(seq)
print(translations)
Find out how many stops in a frame
""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code, make_seq
standard_code = get_code(1)
seq = make_seq("ATGCTAACATAAA", moltype="dna")
stops_frame1 = standard_code.get_stop_indices(seq, start=0)
stops_frame1
.. jupyter-execute::
stop_index = stops_frame1[0]
seq[stop_index : stop_index + 3]
Translate a codon
"""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code, make_seq
standard_code = get_code(1)
standard_code["TTT"]
or get the codons for a single amino acid
.. jupyter-execute::
standard_code["A"]
Look up the amino acid corresponding to a single codon
""""""""""""""""""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code
standard_code = get_code(1)
standard_code["TTT"]
Get all the codons for one amino acid
"""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code
standard_code = get_code(1)
standard_code["A"]
Get all the codons for a group of amino acids
"""""""""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
targets = ["A", "C"]
codons = [standard_code[aa] for aa in targets]
codons
.. jupyter-execute::
flat_list = sum(codons, [])
flat_list
Converting the ``CodonAlphabet`` to codon series
""""""""""""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import get_code
gc = get_code(1)
alphabet = gc.get_alphabet()
print(alphabet)
Obtaining the codons from a ``DnaSequence`` object
""""""""""""""""""""""""""""""""""""""""""""""""""
Use the method ``get_in_motif_size``
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
codons = my_seq.get_in_motif_size(3)
codons
Translating a DNA sequence
""""""""""""""""""""""""""
The defaults for ``get_translation()`` include using the standard genetic code and trimming a terminating stop if it exists.
.. jupyter-execute::
pep = my_seq.get_translation()
pep
Translating a DNA sequence containing stop codons
"""""""""""""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
:hide-code:
from cogent3.core.alphabet import AlphabetError
Making a sequence that contains both internal and terminating stop codons.
.. jupyter-execute::
:raises:
from cogent3 import make_seq
seq = make_seq("ATGTGATGGTAA", name="s1", moltype="dna")
Translating this will fail with default settings.
.. jupyter-execute::
:raises: AlphabetError
pep = seq.get_translation()
Unless you explicitly allow stop codons
.. jupyter-execute::
pep = seq.get_translation(include_stop=True)
pep
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