[Biopython] Is there any Biopython tool to degenerate a nucleotide sequence

[Peter Cock]

Hi Carlos,

Is the input always unambiguous nucleotides? If so should the
output for each "degenerate codon" consider of two unambiguous
nucleotides and a possibly ambiguous IUPAC code for the third
base?

Otherwise you can probably construct alternative answers with
an ambiguity code in the 1st or 2nd position (depending on the
genetic code).

e.g. TTA = Leucine with standard NCBI table 1
Also coding Leucine: TTG, CTT, CTC, CTA, CTG

Possible answer: TTA --> TTR meaning TTA or TTG
Alternative answer: TTA --> YTA meaning TTA or CTA

Peter

On Tue, Jul 28, 2015 at 2:21 PM, Carlos Pena <mycalesis at gmail.com> wrote:
> Dear Biopython members,
>
>
> I want to take a nucleotide string and degenerate those bases that can
> undergo synonymous change.
>
> For example, a string of just one codon.
>
> * Input:  AAC
> * Output:  AAY
>
> Since both AAC and AAT are translated to Asparagine (N) we can
> degenerate this codon to AAY (because the third position could produce a
> synonymous change).
>
> This is already solved in the Perl library Degen
> http://www.phylotools.com/ptdegendocumentation.htm
>
> I could use some glue to execute this Perl code from Python but
> I cannot include this library in my project because they are using the
> GPL license while I use BSD.
>
> So I thought asking around before writing a Python script to do this for me.
>
>
> thanks for any pointers,
>
>
> carlos
>
>
> --
> Dr. Carlos Peña
> Laboratory of Genetics
> Department of Biology
> University of Turku
> 20014 Turku
> FINLAND
>
> * Associated Editor, Revista Peruana de Biología
> http://revistasinvestigacion.unmsm.edu.pe/index.php/rpb
> * The Nymphalidae Systematics Group
> http://nymphalidae.net
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