F: 50 -CTKTTGGGYYCCCKGRYYG-30
Rev: 50-CGCGTCCACTMTCCAGTTCTC-30
These are primers for NGS sequencing of bifidobacteria from a publication.
If you substitute, for example K, with G or T then you get two sets of different F primers and if you substitute other letters with corresponding nucleotides you get many more. So, how do you go about it? Do you test all variants? Or there is an easier way to design degenerate primers?
just design degenerate primers. Normally, the degenerate primers should contain no more than 256 different primers, the less the better. Otherwise it could be very difficult to pick up your target fragment.
Yes, but what bases do I put in place of K or R or Y-that's the question.
you just type K, or R or Y the the location. The primer synthesizing company knows what you mean here.
K=G/T, R=A/G, Y=C/T.
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