[Bioperl-l] Degenerate primer calculation

[Chris Fields]

On Dec 8, 2008, at 9:59 AM, Samantha Thompson wrote:

> 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

Bio::Tools::CodonTable reverse translates, but I don't think it  
accepts patterns.  Maybe a pipeline including Bio::Tools::SeqPattern?   
Might be an interesting programming challenge if it isn't already set  
up for that.

chris