[Bioperl-l] Degenerate primer calculation

Heikki Lehvaslaiho heikki.lehvaslaiho at gmail.com
Fri Mar 13 09:53:55 EDT 2009


Adding your code to Bio::Tools::CodonTable might make it slower. We do
not want that. Test that first.

Even better, why do not put it in as a separate module:



2009/3/11 Bruno Vecchi <vecchi.b at gmail.com>:
> Hi all,
> I wrote a script that reverse translates a Profam-like protein motif
> into its correspondent degenerate nucleotide sequence, using Chris' and
> Brian's suggestions on this thread. You can download it from here:
> http://github.com/brunoV/revtrans-motif/tree/master
> Even though right now it's built as a script, I wrote it thinking of
> adding it as a method; maybe to Bio::Tools::CodonTable.
> What do you think? The script is a thin wrapper over a module
> temporarily named "Revtrans", it already has tests.
> Cheers,
>   Bruno.
>> From: Chris Fields [mailto:cjfields at illinois.edu]
>> Sent: 08 December 2008 16:41
>> To: Samantha Thompson
>> Cc: bioperl-l List
>> Subject: Re: [Bioperl-l] Degenerate primer calculation
>> 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
>> ...........
>> Hi,
>> I'm trying to have a go at solving this problem and I'm looking at
>> Bio::Tools::SeqPattern. What I would like to be able to obtain from a
>> motif is a list of all the sequences that that sequence could correspond
>> to. E.g IKL[GP]NM could be IKLGNM or IKLPNM ... so I take both of these
>> sequences and turn them into degenerate codons for each amino acid. The
>> complicated part (I thought) here is creating a degenerate codon that
>> corresponds to either G or P. The way I will do this is by producing
>> each of the 3 degenerate bases and creating a new codon by creating each
>> of the 3 degenerate bases separately based on a 2D matrix which contains
>> the result of 'crossing' each of the nucleotide bases of the degenerate
>> code with each other. So when you cross the codon for G (GGN) with the
>> codon for P (CCN) you get a codon that contains the degeneracy of both
>> (SSN). So then you have a degenerate nucleotide sequence for your
>> peptide motif.
>> I have written this part already but I am wondering about the expand
>> function of Bio::Tools::SeqPattern . I'm not quite sure what it means by
>> the expanded sequence (if there is just one?) that it returns. I'm
>> trying to get every possible permutation of the motif is there any
>> function that does this or will I have to write one to parse it myself?
>> .....
>> This would be great, but what would make things even better would be if
>> I could take multiple sequence alignments and produce patterns/motifs
>> from them. Is there a part of BioPerl that does something like this?
>> Thanks,
>> Sam
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Heikki Lehvaslaiho - heikki lehvaslaiho gmail com
Sent from: London Greater London United Kingdom.

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