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

[Roy Chaudhuri]

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