Best approach to quantify specific bacteria strain
0
0
Entering edit mode
4.3 years ago
CY ▴ 610

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 • 1.1k views
ADD COMMENT
2
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1876 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6