# 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

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Available genetic codes

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Trees