[Biopython-dev] back_table in Bio.Data.CodonTable

Peter Cock p.j.a.cock at googlemail.com
Wed Aug 1 10:43:59 UTC 2012

On Tue, Jul 31, 2012 at 8:07 PM, Jeff Hussmann <jeff.hussmann at gmail.com> wrote:
> It seems desirable to have each amino acid's list of codons be given
> in a deterministic order. I have been sorting lexicographically using
> the ordering 'TCAG'. This is referred to as the 'conventional
> ordering' in CodonTable.__str__.

Lexical sorting (i.e. using Python's sort on a list of codons) seems best,
it is simple and predictable.

> The most flexible solution would be
> to take the ordering from self.nucleotide_alphabet.letters, but this
> would give 'GATC' for any CodonTable using IUPAC.unambiguous_dna as
> its nucleotide alphabet. Are there any Biopython-wide conventions
> here?

I'm not sure why the alphabets used that particular order over another.


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