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Best approach to quantify specific bacteria strain

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!

qpcr snp sequence alignment
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written by CY CY

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

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written by harold.smith.tarheel harold.smith.tarheel

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