[Bio-software] Re: degenerated codons

darked via bio-soft%40net.bio.net (by darek.kedra from gmail.com)
Wed Jun 13 11:19:16 EST 2007

On May 4, 9:26 am, "Sebastian Grimm" <sebastian.gr... from gmail.com>
> Betreff:
> Hi group,
> I am looking for a program (win95 or on the web) that can convert
> degenerated codons into all posible amino acids and also calculates the
> combinatorical posibilliy for each amino acid. Please, tell me if you
> have heard of such a program.
> Thanks, Matthias
> Hi Matthias!
> So etwas suche ich auch. Hast du eine Antwort bekommen?
> Viele Gruesse,
> Sebastian.

Both BioPerl and transeq from EMBOSS will translate IUPAC codes, but
for degenerated sequences you will get X as an aminoacid not a
specific one. So if your stretch of degenerate nucleotides is not too
long you may generate a fasta file with actg nucleotides only,
translate it using transeq, then count frequencies of aminoacids at a
given position.

Darek Kedra

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