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 Helix Studio, the Genome IDE for CRISPR teams.
System of Record →Section 1
What the tool is
The PAM Scanner highlights valid PAMs for your chosen nuclease in real time as you pan and zoom the genome.
Section 2
Why scientists care
Simple PAM discovery is still split between web calculators and manual searches.
Section 3
How Helix solves it
Preset motifs for SpCas9, SaCas9, Cas12a, Cas12f, plus custom regex-like patterns
Section 4
How the algorithm works
Motif searches run on compiled pattern matchers with strand awareness for speed.
Section 5
Try it in Helix Studio
Open any FASTA or reference segment, select your nuclease, and watch PAMs light up.
Section 6
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.