Anyone here used MISA with Primer3 for marker generation?

[TissueCrafter]

I'm wondering if anyone's used MISA along with Primer3 to create molecular markers. What sequences did you go with, how did you set it up, and what results did you see?

I'd love to share experiences, tips, or any challenges you faced

 

[Emali_day]

We used MISA with Primer3 for SSR marker development at work like last year and I cant really remember a lot of details but it was in a few plant species, I think we set MISA to detect di to hexanucleotide repeats, with default thresholds (e.g. 6 for di, 5 for tri), then used the output to feed Primer3 for primer design. The biggest thing was watching for primers that land too close to the repeat edges or sit on low complexity flanks, cos they can be a pain during PCR.

 

[matrix|maker]

It really reminds me of a project I worked on regarding wild rice populations. We also used MISA and Primer3, and I still vividly recall the struggle with primers landing in those tricky low complexity regions. I had a whole series of PCRs fail one after the other because of it. I quickly learned to double-check those flanking sequences before finalizing anything. It's nice to know others have faced the same challenges

 

[TropicalMe]

I've used MISA with Primer3 a few times and I usually start with default SSR motifs and let Primer3 design primers around them. Works fine for simple repeats, but tricky motifs sometimes needed manual tweaking.