Question: mutiple primer check algorithm
gravatar for J.F.Jiang
5.5 years ago by
J.F.Jiang830 wrote:

Hi all,

I am designing primers for multiple-PCR. Actually, we allowed 20 primers in a well, in which we should check the possibility of dimer, hairpin, and amplicon formation among pre-designed primers.

I get the perl script of Max 3' Complementarity from primer 3, which could be used to determin the likehood of primer dimers.

We have 200 paired primers in hand, which should be seperated into 10 groups. In each groups, we need to guarantee the pooled primers could be correctly amplified.

Is there any existed perl program for whole process or for hairpin only? I searched, but can not get it.



pcr primer dimer hairpin • 2.0k views
ADD COMMENTlink modified 5.2 years ago by Wubin Qu160 • written 5.5 years ago by J.F.Jiang830

Asking only for programs in a specific language will limit the responses in both quantity and quality.  Why would you do that?

ADD REPLYlink written 5.5 years ago by Brian Bushnell17k
gravatar for Wubin Qu
5.2 years ago by
Wubin Qu160
Wubin Qu160 wrote:

Primer3 code package has a program named ntthal which can check hairpins, but that's not written in Perl.

ADD COMMENTlink written 5.2 years ago by Wubin Qu160
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