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

From a string

This can also be applied to a numpy array.

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

Translate all six frames

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

Getting the alphabet for the genetic code

The default for the get_alphabet() method is to return an alphabet representing just the sense codons (a SenseCodonAlphabet instance).

Setting include_stop=True returns all codons.

You can also include “gap state” (i.e. "---") or “missing state” ("???") codons with the arguments include_gap and include_missing respectively.