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

Fields, Christopher J cjfields at illinois.edu
Mon Feb 27 16:18:54 EST 2012


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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