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

Frank Schwach fs5 at sanger.ac.uk
Mon Feb 27 04:48:30 EST 2012


Hi Florent,

I was recently thiking about something similar when adding 
delete/insert/ligate methods to Bio:;SeqUtils (now in bioperl-live). I 
was about to add a PCR method as well and I think it would fit in with 
that module. Similar to other methods in this module, the PCR method 
should be able to handle sequence features and annotations, so that the 
amplicons are fully annotated. I'd be willing to discuss this further 
and work with yuo on that if you like.

Cheers,

Frank


On 26/02/12 06:44, 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?
>
> 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
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