Detect repeats problematic for PCR

Question

[mschmid]

I have a couple of target genomic regions from bacteria. Now I want to check if they are suitable to be templates for a PCR reaction (diagnostics). Which types of repeats are problematic for designing PCR primers?

I can think of several types of repeats which could be problematic for design of PCR: 1) Interspersed repeats within a target genomic region. Detect with Nucmer? 2) Tandem repeats within a target genomic region. For example detect with equicktandem? 3) General low complexity regions within a target genomic region. Detect with dustmasker? 4) Areas in the target region which are similar to other sites on the genome. Detect with Nucmer?

Do you in general test for repeats? What is your strategy and how do you do this? What do you think of my suggestions for tools and what would be a better replacement?

Answer 1

[ATpoint]

I would try to feed these regions into PrimerBLAST and see if it returns suitable primers. Provide the respective bacterial genome as a background. From there on you'll probably anyway need to check by experiment if it works. PCR is not very predictable in many cases unfortunately (in my experience, even if you use PrimerBLAST or similar).

:)