Question: Blocking primer design software?
gravatar for predeus
12 months ago by
predeus820 wrote:

Hello all,

I was wondering if anybody come across any software tools dedicated to the design of blocking primers.

Any suggestions would be appreciated.

ADD COMMENTlink modified 3 months ago by lufiealf0 • written 12 months ago by predeus820

Hello, just curious if you had any luck finding software?

ADD REPLYlink written 3 months ago by lufiealf0

Unfortunately not. If the primer you require is shorter, then you can get away with mapping - I've mapped 15-mers with bowtie2 onto the groups I was interested in (just 16S from SILVA; you need to use -a option, and it's quite slow, so you would need a reasonable computational power).

But 15nt are OK for PNA blockers. For DNA-based oligos people use 18nt and more, and you can't really rely on mapping those k-mers because there are too many. What remains is mapping to a consensus, which is a poor alternative, but should mostly do the job.

ADD REPLYlink written 3 months ago by predeus820
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