[Biopython] Degenerated Codons

Matthias Bernt MatatTHC at gmx.de
Thu Feb 23 11:00:42 UTC 2012


You can probably do that with the codon dictionaries
> provided in Bio.Data.CodonTable (used for translations).
> If you could give some specific examples of input and
> desired output I'm sure we can give you more hints.

You mean the forward_table?

The most important function for me is:
- Input: Codon (sequence of length 3), code table
- Output: X, number of codons coding for the same
  amino acid as the given codon

Building on this it would be easy to implements:
- Input: Codon, code table, X
- Output: true iff there are X codons coding for the same amino acid

Also important (and maybe the core of the other two functions):
- Input: codon
- Output: list of codons coding for the same amino acid

I think this is it. I need to implement these functions anyway.
So maybe you can give me hints how I should implement it.
For my application it would be acceptable to iterate over the
forward_table for each call.
But maybe its possible to modify the backward_table such
that it stores all codons (as list) for a amino acid. For the other
functions building on it (back translation...) it would be possible
to take the first element of the list.


More information about the Biopython mailing list