CRISPR
PAM Scanner Tool
Instantly find NGG and alternative PAMs across any locus.
Scan loci for NGG and custom PAMs with instant genome overlays and handoff to guide design inside Omnis Helix, the Genome IDE for CRISPR teams.
Tool definition
What the tool is
The PAM Scanner highlights valid PAMs for your chosen nuclease in real time as you pan and zoom the genome.
Decision pressure
Why scientists care
Simple PAM discovery is still split between web calculators and manual searches.
Genome IDE fit
How the Genome IDE helps
Preset motifs for SpCas9, SaCas9, Cas12a, Cas12f, plus custom regex-like patterns
Scoring model
How the algorithm works
Motif searches run on compiled pattern matchers with strand awareness for speed.
Evaluation path
Try it in the Genome IDE
Open any FASTA or reference segment, select your nuclease, and watch PAMs light up.
Questions
FAQ
Can I scan plasmids or amplicons?
Yes—upload custom sequences and the scanner treats them like any genome segment.
Do you support degenerate motifs?
Custom motif syntax supports IUPAC codes so you can model engineered PAMs.
Will this slow down large regions?
Scanning is streaming and incremental; even megabase windows stay responsive.