[Bioperl-l] primer selection

[Jonathan M. Manning]

I too have an internal set of scripts that handles primer selection, 
using Bio::Seq objects and primer3, then blasting against E.Coli to 
screen out vector matches.

I'm not entirely convinced about the 'Pair of primers' approach you've 
listed here - I'd favor it being primarily for selection of single left 
or right primers, though these objects could certainly be paired up 
later, and additional 'Assessments' be run on them.

You'll have to get a reply from someone else regarding how it best fits 
into BioPerl, but I'd like to see something like this included, and I'd 
be willing to contribute to it. I was planning a rewrite of my scripts 
anyway... time to modularize.

~Jonathan

Ewan Birney wrote:
> 
> I have been scripting primer design for a while where I find I have 
> better control over
> the heuristics and (importantly) can include BLAST/exonerate matching of 
> a region
> to its own genome to find unique-in-genome areas.
> 
> 
> I know Primer3 is out there, but in some cases, making sure you design a 
> primer in
> a non-duplicated region is more important than getting the right G/C 
> content etc.
> 
>