[BiO BB] Primer BLAST

[Iddo Friedberg]

Bill,

Have you considered downloading and installing BLAST locally, and then 
writing a script to run all your primers and record their scores?

ftp://ftp.ncbi.nih.gov/toolbox/

Iddo


Bill_A_Nussbaumer at bd.com wrote:
> Hi all,
> 
> I'm hoping a method exists that would allow me to align PCR primers against
> the human genome to determine all products that could be amplified if my
> sample contained extracted human DNA.  Theoretically I could BLAST each
> primer with stringent parameters and record the coordinates on the genome
> looking for matches with a Kb or two of one another.  To do that manually
> would be quite tedious, especially when you consider that I'm only really
> interested in matches at the 3' end.
> 
> Anyone know of a way to do this?
> 
> - Bill
> 
> 
> 
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-- 
Iddo Friedberg
The Burnham Institute
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