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"
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.
Translate DNA sequences¶
Conversion to a ProteinSequence
from a DnaSequence
is shown in Translate a DnaSequence to protein.
Translate all six frames¶
Find out how many stops in a frame¶
Translate a codon¶
or get the codons for a single amino acid
Look up the amino acid corresponding to a single codon¶
Get all the codons for one amino acid¶
Get all the codons for a group of amino acids¶
Converting the CodonAlphabet
to codon series¶
Obtaining the codons from a DnaSequence
object¶
Use the method get_in_motif_size
Translating a DNA sequence¶
The defaults for get_translation()
include using the standard genetic code and trimming a terminating stop if it exists.
Translating a DNA sequence containing stop codons¶
Making a sequence that contains both internal and terminating stop codons.
Translating this will fail with default settings.
Unless you explicitly allow stop codons