primer.design, selectivity against other OTUs

Commands in mothur
1

Hi,

My question concerns primer.design - command. I understand it can be used to design primers targeting the OTU of interest (defined by otulabel=). Does it screen the candidate primers against other OTUs? Thus, are the primers selective against the OTUs that are not of interest?

Best,
Antti Rissanen, PhD
Tampere University of Technology
Tampere, Finland

2

I would be happy to explain the inner workings on the primer.design command.

  1. Mothur finds consensus sequences for each OTU.
  2. Mothur finds all the primers for the OTU selected. If you set the mintm or maxtm parameters mothur may screen out some of the primers for you.
  3. Mothur scans each OTU’s consensus sequence looking for the primers from the “selected” OTU’s consensus sequence. If primers are found, they are reported and the OTU is removed.

Does this answer your question?