[BiO BB] primer pairings

[Bela Tiwari]

>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:

http://www.wisc.edu/genetics/CATG/amplify/ 

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

http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html

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
unfortunately.)


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
references)

1) The primer list at the HGMP:

http://www.hgmp.mrc.ac.uk/GenomeWeb/nuc-primer.html


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

http://www.bbsrc.ac.uk/molbiol/reviews.html


good luck. 


Bela


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