mutiple primer check algorithm

Question

[J.F.Jiang]

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 determine the likelihood 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.

Thanks

[Brian Bushnell]

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

Answer 1

[Wubin Qu]

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