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 make_seq, get_code
>>> 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 make_seq, get_code
>>> standard_code = get_code(1)
>>> seq = make_seq('ATGCTAACATAAA', moltype="dna")
>>> stops_frame1 = standard_code.get_stop_indices(seq, start=0)
>>> stops_frame1
[9]
>>> stop_index = stops_frame1[0]
>>> seq[stop_index:stop_index+3]
DnaSequence(TAA)
Translate a codon¶
>>> from cogent3 import make_seq, get_code
>>> 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'
Or 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']
For a group of amino acids¶
>>> targets = ['A','C']
>>> codons = [standard_code[aa] for aa in targets]
>>> codons
[['GCT', 'GCC', 'GCA', 'GCG'], ['TGT', 'TGC']]
>>> 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())
['AAA', 'AAC', 'AAG', 'AAT'...
>>> len(my_seq.codon_alphabet())
61
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']
You can’t translate a sequence that contains a stop codon.
>>> pep = my_seq.get_translation()
Traceback (most recent call last):
cogent3.core.alphabet.AlphabetError: TAA
Remove the 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())
>my_gene
MHW
>>> print(type(pep))
<class 'cogent3.core.sequence.ProteinSequence'>
Or we can just grab the correct slice from the DnaSequence
object¶
>>> 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