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

[Paul Gordon]

> 	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?

We also have hairpin binding and arbitrary secondary binding constraints
in the program I wrote, plus an option to pick the 2nd or 3rd, etc.
optimal primer in case the first one fails.  But Eitan's right, too many
or obscure parameters reduces the usability/reliability of a program.  For
a lightweight module, David would probably want to stick to basic
parameters, sacrificing extreme flexibility for simplicity of "normal"
use.

> 	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 guess if all of the functionality you want is in Primer3, a SWIG
(www.swig.org) wrapping and maybe a little cleanup of the generated module
would do the trick.  Is that considered "lightweight" enough?

> > 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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