Question: Designing Primers For Microsatellites In Long Scaffolds
1
gravatar for figo
5.6 years ago by
figo200
figo200 wrote:

Hi All

I have very long scaffolds in megabases, I figured out all the microsatellites in it. Now I want to design primers for those microsatellites but as my sequences are very long it is taking too much of time to run the primer3. Any one knows a better way to design primers in scaffolds as my scaffolds are very big.

Best

• 2.0k views
ADD COMMENTlink modified 2.1 years ago by Felix Francis490 • written 5.6 years ago by figo200
2
gravatar for Michael Dondrup
5.6 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

Why should you input the full contig, if your aim is to amplify a defined region. Could you try to extract only the flanking regions of each microsatelite, and use these? As the primers shouldn't overlap with the repeat region itself, you could also replace it with a small placeholder of fixed length.

ADD COMMENTlink written 5.6 years ago by Michael Dondrup46k
1
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

NCBI primer blast ? http://www.ncbi.nlm.nih.gov/tools/primer-blast/

ADD COMMENTlink written 5.6 years ago by Pierre Lindenbaum119k
0
gravatar for Felix Francis
2.1 years ago by
Felix Francis490
United States/University of Delaware
Felix Francis490 wrote:

Here is a primer design tool for tiled amplicon sequencing (includes multiplexing):

Manuscript: http://www.nature.com/articles/srep44437

https://github.com/drmaize/ThermoAlign

ADD COMMENTlink written 2.1 years ago by Felix Francis490
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