Bioperl: Project volunteer: Sequence/PCR primers (Tm, primer design, etc.)

[Eitan Rubin]

	I've written a mathematical/simulation article on PCR primer specificity,
and I read what little literature there was on the subject back in 1996.
Primer design is the art of parameters: how important is preventing
self-priming compared to minimizing primer-primer temperature difference? Do
you prefer getting to the upper limits of product size, or to the lower
limits of annealing temperature? You don't want to write a program no one
can use without guessing what's the right parameters. On the other hand, if
you simply copy the parameters from some program, than why not just use it?
	I have seen people write their own primer design programs, which failed to
produce satisfactory primers. Primer3 of whitehead, on the other hand, is an
open source non-perl program that proved itself a zillion times in the human
genome project and in my hands, so a wrap around (pretty much like blast)
seems a more reasonable option.
I have written a *very* crude perl script aimed at allowing high-throughput
primer design with Primer3. It will not be useful to bioperl since it was my
first real perl program, but it taught me it is very easy to write such
code. And since primer3 is open source, it's easy to keep it stable.


   Eitan


> -----Original Message-----
> From: owner-vsns-bcd-perl@lists.uni-bielefeld.de
> [mailto:owner-vsns-bcd-perl@lists.uni-bielefeld.de]On Behalf Of
> shivakd@slip.net
> Sent: Tuesday, January 11, 2000 10:33 AM
> To: vsns-bcd-perl@lists.uni-bielefeld.de
> Subject: Bioperl: Project volunteer: Sequence/PCR primers (Tm,
> primer design, etc.)
>
>
> I'm a fledgling perl programmer / biologist looking for an interesting,
> do-able project to contribute to Bioperl.  I am interested in working on
> the "lightweight" primer design analysis (as stated on
> http://bio.perl.org/Projects/Sequence/: "Desirable lightweight
> analyses not
> yet written-- Sequence/PCR primers (Tm, primer design, etc.)").
> Due to the
> recent revamping proposal of the Bio::Seq module, I'm wondering if this is
> a good choice.  Would writing a primer design toolset as a
> Bio::Tools::Primers module would be the best choice?
>
> Comments, suggestions, corrections, code, and encouragement is welcome.
>
> Thanks,
>
> David Shivak
>
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