Question: Best approach to quantify specific bacteria strain
0
gravatar for CY
2.4 years ago by
CY460
United States
CY460 wrote:

I have a project asking to quantify a specific bacteria strain from a sample using qPCR. First I need to design one or more primers. Since I am new to primer design, I got several questions while designing the protocol.

  1. Should I use 16S hypervariable region as PCR template?
  2. Should I use Primer-BLAST as primer design tool? and should I used Genome database (reference assembly from selected organisms) as database for the design?
  3. If I got multiple hits, does it mean they are qualified as PCR primers?
  4. How many pairs of primer should I use to be sufficient to specifically target particular strain?

Can anyone has this kind of experience share some insight? Really appreciate!

snp qpcr alignment sequence • 729 views
ADD COMMENTlink written 2.4 years ago by CY460
2

This isn't really a bioinformatics question. You might get more useful responses from the SEQanswers forum (mention that it's cross-posted here).

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by harold.smith.tarheel4.5k
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