Translate DNA sequences¶

from cogent3 import get_code

standard_code = get_code(1)
standard_code.translate("TTTGCAAAC")

'FAN'

Conversion to a ProteinSequence from a DnaSequence is shown in Translate a DnaSequence to protein.

Translate all six frames¶

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)

['MLT*', 'C*HK', 'ANI', 'FMLA', 'LC*H', 'YVS']

Find out how many stops in a frame¶

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
stop_index = stops_frame1[0]
seq[stop_index : stop_index + 3]

	0
None	TAA

3 DnaSequence

Translate a codon¶

from cogent3 import get_code, make_seq

standard_code = get_code(1)
standard_code["TTT"]

'F'

or get the codons for a single amino acid

standard_code["A"]

['GCT', 'GCC', 'GCA', 'GCG']

Look up the amino acid corresponding to a single codon¶

from cogent3 import get_code

standard_code = get_code(1)
standard_code["TTT"]

'F'

Get all the codons for one amino acid¶

from cogent3 import get_code

standard_code = get_code(1)
standard_code["A"]

['GCT', 'GCC', 'GCA', 'GCG']

Get all the codons for a group of amino acids¶

targets = ["A", "C"]
codons = [standard_code[aa] for aa in targets]
codons
flat_list = sum(codons, [])
flat_list

['GCT', 'GCC', 'GCA', 'GCG', 'TGT', 'TGC']

Converting the `CodonAlphabet` to codon series¶

from cogent3 import make_seq

my_seq = make_seq("AGTACACTGGTT", moltype="dna")
sorted(my_seq.codon_alphabet())
len(my_seq.codon_alphabet())

Obtaining the codons from a `DnaSequence` object¶

Use the method get_in_motif_size

from cogent3 import make_seq

my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
codons = my_seq.get_in_motif_size(3)
print(codons)

['ATG', 'CAC', 'TGG', 'TAA']

Translating a DNA sequence with a terminating stop codon¶

You can’t translate a sequence that contains a stop codon.

pep = my_seq.get_translation()

---------------------------------------------------------------------------
AlphabetError                             Traceback (most recent call last)
Cell In[12], line 1
----> 1 pep = my_seq.get_translation()

File ~/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.9/site-packages/cogent3/core/sequence.py:1316, in NucleicAcidSequence.get_translation(self, gc, incomplete_ok)
   1314 orig_codon = self._seq[posn : posn + 3]
   1315 try:
-> 1316     resolved = codon_alphabet.resolve_ambiguity(orig_codon)
   1317 except AlphabetError:
   1318     if not incomplete_ok or "-" not in orig_codon:

File ~/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.9/site-packages/cogent3/core/alphabet.py:710, in Alphabet.resolve_ambiguity(self, ambig_motif)
    707 motif_set = [motif for motif in motif_set if motif in self._quick_motifset]
    709 if not motif_set:
--> 710     raise AlphabetError(ambig_motif)
    712 return tuple(motif_set)

AlphabetError: TAA

By removing the trailing stop codon first¶

from cogent3 import make_seq

my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
seq = my_seq.trim_stop_codon()
pep = seq.get_translation()
print(pep.to_fasta())
print(type(pep))

>my_gene
MHW

<class 'cogent3.core.sequence.ProteinSequence'>

By slicing the `DnaSequence` first¶

from cogent3 import make_seq

my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna")
pep = my_seq[:-3].get_translation()
print(pep.to_fasta())

>my_gene
QMY