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# 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.