On May 4, 9:26 am, "Sebastian Grimm" <sebastian.gr... from gmail.com>
wrote:
> 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
wikiomics.org
