Designing Primers For Microsatellites In Long Scaffolds

Question

[figo]

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

Answer 1

[Michael]

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.

Answer 2

[Pierre Lindenbaum]

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

Answer 3

[Felix Francis]

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

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

https://github.com/drmaize/ThermoAlign