Utilities
PCR Primer Designer for Genome Editing
Design PCR primers that align with CRISPR and Prime Editing assays.
Design PCR primers centered on CRISPR and Prime Editing assays with Tm/GC balance and QC in Omnis Helix, the Genome IDE.
Tool definition
What the tool is
The PCR Primer Designer proposes primer pairs around your edit site with Tm/GC balance and amplicon size tuned for downstream analysis.
Decision pressure
Why scientists care
Generic primer tools ignore edit windows, leading to assays that miss the effect you care about.
Genome IDE fit
How the Genome IDE helps
Adjustable amplicon spans centered on cuts or RTT windows
Scoring model
How the algorithm works
Primer candidates are generated with constraint solving for Tm, GC, and amplicon size; problematic motifs are filtered out.
Evaluation path
Try it in the Genome IDE
Choose your guide or pegRNA, set desired amplicon size, and select from QC-ranked primer pairs.
Questions
FAQ
Can I include barcodes/adapters?
Yes—toggle adapters and Helix will account for them in Tm calculations.
Do you support multiplex panels?
We score cross-dimers and warn about overlapping amplicons before you finalize a panel.
How are primers delivered?
CSV/FASTA plus annotated PDFs ready for ordering.