Protocol Online logo
Top : Forum Archives: : Real-Time PCR

free software to examine if two primers will make dimers - (Nov/16/2005 )

hi
i need a free software to test some primers sets i have to choose ideal ones to use

-husam-

I am wonderin if there is one in the first place ? Ans I do not think there will be a set of primer that 100% will not self-dimerize..but maybe someone can further tell more about it

-gxelan-

Hi there
Try Net primer, its free and available online (not as a download). Its on the premierbiosoft.com website. Using these and paid for software tools are no guarantee your assay will work though. I have used primers with fairly bad dimer results but have worked very well. Mpst people would advise to use Sybr green instead of a specific probe first as well to get a good look at your assay but dont forget there maybe interactions with a specific probe as well.
Parky

QUOTE (husam @ Nov 17 2005, 05:35 AM)
hi
i need a free software to test some primers sets i have to choose ideal ones to use

-Parky-

Guys,

there are lots of free software on the web for primer design etc.

An excellent on-line program for primer design and analysing primers is IDT SciTools - http://www.idtdna.com/SciTools/SciTools.aspx

Use Oligo Analyzer to check for primer dimers, primer-primer complexes and hairpin bends. PrimerQuest is one of the best programs I have used on-line for primer design.

Hope this helps,

AussieUSA.

-AussieUSA-