[Bioperl-l] Fate of Bio::Tools::PCRSimulation

Florent Angly florent.angly at gmail.com
Thu Mar 1 19:12:19 EST 2012

Thanks for everybody's feedback.

I am looking at existing modules to hold template sequence, amplicon 
sequence and primer information. There is the Bio::SeqFeature::Primer 
and Bio::Seq::PrimedSeq. At the moment the PrimedSeq object places 
Primer objects on the target sequence. I have been looking at refreshing 
these modules (they are quite old), add some sanity to them and make 
sure they are suitable for a generic implementation of PCR (or amplicon 
search, which I find a more suitable name since it is a far cry from 
simulating PCR cycles, etc).

I will make a remote branch today to make it easier for interested 
parties to experiment and contribute.

As you can see Chris, the amplicon search feature would use two existing 
bioperl-live modules and only add one, tentatively in the 
Bio::Tools::AmpliconSearch namespace. I am not convinced that this 
warrants a separate distro.


On 01/03/12 01:23, Fields, Christopher J wrote:
> Seems like it was meant to be added at some point but was never committed.  Definitely not in the github history for 1.3.x, this commit corresponds to the v1.3.4 tag:
>     https://github.com/bioperl/bioperl-live/tree/0a67fa444eb19a70876017607f70ab72be38755a
> and it's not there.
> I agree with Roy, it would be nice to somehow make this a little more generic or pluggable on how it maps primers (maybe with a default pure perl method).  I also think this shouldn't be bound to bioperl-live considering our current plans, it would best happen in a separate repo.
> chris
> On Feb 29, 2012, at 9:06 AM, Roy Chaudhuri wrote:
>> The code for Bio::Tools::PCRSimulation can be downloaded as part of this archive:
>> http://www.salmonella.org/bioperl/primer3_v0.3.tgz
>> (There's supposedly a more recent version here:
>> http://www.salmonella.org/bioperl/nucleotide_analyses.tgz
>> but that file seems to be truncated).
>> I have no idea how much would be salvagable. It seems to just use index to map the primers to the sequence, I guess it would make more sense to at least give the option of something more sophisticated like Primer3, BLAST or even a short read mapper.
>> Cheers,
>> Roy.
>> On 27/02/2012 21:18, Fields, Christopher J wrote:
>>> On Feb 26, 2012, at 12:44 AM, Florent Angly wrote:
>>>> Hi all,
>>>> I am interested in the Bio::Tools::PCRSimulation module. Supposedly
>>>> it was added to Bioperl 0.3 and is also mentionned in the
>>>> Bio::PrimedSeq module. However, I cannot find in the current
>>>> Bioperl codebase. Any idea where it went?
>>> No idea; I can't find it anywhere in the code base either, and the
>>> github repo contains history going back to the original CVS repo.
>>> You can try contacting the author, possibly.
>>>> The reason I am asking is because I have some code to do silico PCR
>>>> using regular expressions. I wanted to modularize my code more and
>>>> make it into a module for Bioperl. Of course, if there is something
>>>> similar in Bioperl already, I need to have a look at it. If there
>>>> is nothing similar, what namespace do you suggest to use?
>>>> Bio::Tools::AmpliconExtractor? Bio::Tools::AmpliconSearch?
>>>> Bio::Tools::InSilicoPCR?
>>>> Thanks,
>>>> Florent
>>> Maybe the last (InSilicoPCR).
>>> chris
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