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Primer design with GCG

Bruce Roe broe at aardvark.ucs.uoknor.edu
Sat Jan 15 15:14:00 EST 1994


In article <2h4qgu$h0r at news.u.washington.edu>, michaelr at u.washington.edu (Michael Robertson) writes...
>I am designing primers for PCR to amplify a region in the p24 regio of 
>the HIV Gag protein.  Is there a program in GCG that will 
>allow me to test my primers against known HIV sequences to make sure I 
>will not be amplifying other regions of the virus?
> 
Once you've got your primer designed, try:

	FINDPATTERN /mismatch=3

That, on the VAX version of GCG will list all the matches in your target
sequence, in your case HIV, with mismatches up to and including 3.
With a 20+mer pcr primer, and a resonable annealing temperature, not
much product should be seen from >3 mismatches.
Cheers.........bruce
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 \  Bruce A. Roe              Department of Chemistry and Biochemistry /
 /  University of Oklahoma    INTERNET:  BROE at aardvark.ucs.uoknor.edu  \
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