[Bioperl-l] Degenerate primer calculation

Chris Fields cjfields at illinois.edu
Tue Dec 9 00:54:28 EST 2008

An aside, but Higher Order Perl describes some nice memory-efficient  
ways to achieve this (using an iterator or a stream IIRC).  Might be  
worth investigating.


On Dec 8, 2008, at 10:47 PM, Brian Osborne wrote:

> Sam,
> 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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