Primer Specificity

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Primer Specificity

Postby Is Tr » Jan 30 2018 10:39 am

Hey there,

I would like to double check, where in the genome my primers bind. However, I have a primer pool and wobble bases. How do I check primer specificity given these hurdles? I have not designed the primers.

Looking forward to responses!
Is Tr
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Re: Primer Specificity

Postby 29yrsExperience » Feb 01 2018 4:07 pm

Hi Is Tr,

You can probably make use of the Primer-BLAST tool at NCBI (home of GenBank). It can help you design primers or check the uniqueness of primers you already have the sequence for. I’m not sure about wobble bases (degenerate primers) but you might be able to enter them by using the standard nucleotide ambiguity code (ex. Y means pyrimidine C or T). Here is a link to the primer BLAST page:

https://www.ncbi.nlm.nih.gov/tools/prim ... ultiSensor

Good luck.
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