fastest method to get potential amplicons based on paired-primers

Question

[J.F.Jiang]

Hi all,

Generally, we can use tools such as primer3 to design the available primers for PCR.

However, sometimes the primer will be located in repeat region, which might lead to non-specific amplicons.

My question is how to get all potential amplicons for this pair primers across the whole genome except to blast for each primer.

Thanks

Answer 1

[Wubin Qu]

MFEprimer can do that.

Answer 2

[Irsan]

If you use NCBI primerblast (which is a primer3 implementation) you get a comprehensive overview of non-intended/aspecific amplicons

[bill-zt]

However primerblast is only available as a web interface, no standalone program