[BiO BB] Primer BLAST

Iddo Friedberg idoerg at burnham.org
Thu Nov 21 14:26:40 EST 2002


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



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
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

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