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

Roy Chaudhuri rrc22 at cam.ac.uk
Wed Feb 29 10:06:23 EST 2012

The code for Bio::Tools::PCRSimulation can be downloaded as part of this 

(There's supposedly a more recent version here:
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.


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
> _______________________________________________ Bioperl-l mailing
> list Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list