[BiO BB] Primer BLAST

Philipp Pagel p.pagel at gsf.de
Fri Nov 22 03:20:14 EST 2002


> 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.
You don't have to use the Web-BLAST at NCBI - just download the BLAST
program and run it on your machine. With a little Perl (or Python or
...) magic you can extract the information you need.

You'll find the BLAST program here:


And the databases are here:


If for some reason you can't or don't want to run BLAST locally you can
also access the NCBI BLAST server directly in your script. Look at 

netblast (blastcl3): ftp://ftp.ncbi.nih.gov/blast/blastcl3/


Bioperl: http://bioperl.org/


Dr. Philipp Pagel                                    Tel.  +49-89-3187-3675
Institute for Bioinformatics / MIPS                  Fax.  +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg

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