Question: fastest method to get potential amplicons based on paired-primers
0
gravatar for J.F.Jiang
3.4 years ago by
J.F.Jiang700
China
J.F.Jiang700 wrote:

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

primer amplicon • 1.3k views
ADD COMMENTlink modified 3.0 years ago by Irsan6.6k • written 3.4 years ago by J.F.Jiang700
0
gravatar for Wubin Qu
3.0 years ago by
Wubin Qu150
China
Wubin Qu150 wrote:

MFEprimer (http://www.mfeprimer.com/) can do that.

ADD COMMENTlink modified 11 months ago • written 3.0 years ago by Wubin Qu150
0
gravatar for Irsan
3.0 years ago by
Irsan6.6k
Amsterdam
Irsan6.6k wrote:
If you use NCBI primerblast (which is a primer3 implementation) you get a comprehensive overview of non-intended/aspecific amplicons
ADD COMMENTlink written 3.0 years ago by Irsan6.6k

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

ADD REPLYlink written 12 months ago by bill-zt40
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