[BiO BB] primer pairings

Bela Tiwari btiwari at molbiol.ox.ac.uk
Tue Mar 13 10:56:43 EST 2001

>I need a free software or internet site for designing primers.
>especially, I need a program that shows potential pairings of a primer in
>the given sequence. I mean, I paste the sequence into the program window and
>also I paste the primer then this program calculates and shows potential
>pairings  on the pasted sequence and on its complementary sequence. Thank
>you very much...

My favorite program for this (when I used to do it!) was a Mac program
called Amplify. Its available, I believe, from:


If you don't have access to a Mac, there is an applet at 


which will test two primers against themselves and each other for
hairpins, repeats, dimer formation, etc, etc. However, I don't think you
can check for where along a sequence your primers might bind  using this
site. (If you do use a Mac, you probably won't be able to use this site

Other than that I'll just give you a couple of sites that list various
primer programs that are out there (which I personally find useful

1) The primer list at the HGMP:


2) There are reviews of various primer packages, (some free and some not)


good luck. 


Dr. Bela Tiwari                Bioinformatics Officer
OU Bioinformatics Centre          
South Parks Road,                  01865 (2)75507 
Oxford  OX1 3RE               http://www.molbiol.ox.ac.uk

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