Question: Detect repeats problematic for PCR
0
gravatar for mschmid
5 months ago by
mschmid150
Switzerland
mschmid150 wrote:

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?

prc repeats • 226 views
ADD COMMENTlink written 5 months ago by mschmid150
6
gravatar for ATpoint
5 months ago by
ATpoint31k
Germany
ATpoint31k wrote:

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).

:)

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ADD COMMENTlink modified 5 months ago • written 5 months ago by ATpoint31k
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