[Bioperl-l] Degenerate primer calculation

Brian Osborne bosborne11 at verizon.net
Mon Dec 8 23:47:21 EST 2008


There's reverse_translate_all() in Bio::Tools::CodonTable, and there's  
also expand() in Bio::Tools::SeqPattern, this should be able to take  
any degenerate nucleotide symbol and give the you [GATC], I think. You  
could use both of these. It seems that what's missing is a method that  
parses the Prosite-style motif, and you would have to supply that and  
any code that could transform the various data structures that are  
created. Interesting problem.

If you do create code to do this please provide it to Bioperl as a  
script or as methods, this would be _very_ useful.

Brian O.

On Dec 8, 2008, at 10:59 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
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