Blocking primer design software?

Question

[predeus]

Hello all,

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

Any suggestions would be appreciated.

[lufiealf]

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

[predeus]

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.