Primer Specificity

Go to the profile of is tr
Jan 30, 2018
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1

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!

1 Comments

Go to the profile of OldCloner
OldCloner 5 months ago

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/primer-blast/index.cgi?LINK_LOC=MultiSensor

Good luck.