multiplex primers - (May/04/2004 )

Hello Forum users, I have a problem with my multiplex PCR. What is the best, in your opinion, tool to check their cross homology? Thank u in advance for any tips.

-Gosiatok-

QUOTE

Once you get into multiplex PCR reactions with several sets of different primers working simultaneously in a single amplification tube making different products, forget it; no software can realistically predict what is going to happen.
http://www.med.nyu.edu/rcr/rcr/course/primer.html

I would suggest that you check it manually by blasting genome databases. Try the UCSC genome database and Blat tool ( http://genome.ucsc.edu/cgi-bin/hgBlat ) which is fast and easy to use.

-sage-

Thank you very much, Sage. I expected that kind of advice unfortunately . I'm quite depressed, I have over 20 pairs of primers to check manually! Thanks for the web links. Have a nice a day!

-Gosiatok-

Hello!
You can try to check your primers with Primer Premier 5.
this software is available on

-gavri-

Hello!
You can try to check your primers with Primer Premier 5.
this software is available on
http://premierbiosoft.com/crm/jsp/com/pbi/...ProductList.jsp

Sorry, my previous post was not complete
Hope it helps.

Regards

-gavri-

The correct link to download Primer Premier5 is
http://premierbiosoft.com/crm/jsp/com/pbi/...ProductList.jsp

One can download the program by just entering the email and from the above link and request for a time limited key.

nevin

-Nevin-

You may try

http://www.changbioscience.com/primo/primoml.html

Click on the "Check" button next to "Check primer-primer dimers"

-laojun-