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

[Carlos Pena]

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