[Bioperl-l] Degenerate primer calculation

[Samantha Thompson]

Hi,

 

I also have another similar sequence analysis/primer problem.

What I'd like to do is produce degenerate primers from amino acid
sequences.

What I did initially was take the codon usage table and rewrite it in a
hash in perl in the form of degenerate codon usage e.g Lysine/K would be
AAR, its reverse complement would be YTT. So my form then takes an amino
acid sequence (derived as a consensus from multiple the alignment of
homologous proteins) and converts them into degenerate codons and then
that degenerate primer (actually several primers synthesised with
different bases pooled together), in order to search for homologues to
the protein in unsequenced organisms.

I would like to improve this by being able to take a consensus described
more in the form of a Prosite motif (I think thats the right one) such
as [TS]YW[RKSD] and then develop a degenerate nucleotide sequence
corresponding to this.

So I'm wondering if bioperl contains anything like this (both prosite
motif format parsing and degenerate code from multiple alignments or
such a motif), or if I need to write this myself (which I want to if it
doesn't exist already).

 

Thanks again,

 

Sam