About Restriction Sites · how to use, FAQ ▾
This scan runs inside SeqStudio, SeqBench's full sequence and plasmid editor: paste or type a DNA sequence below and the Restriction sites panel scans all 49 curated common enzymes live as you edit, with IUPAC-aware matching for degenerate recognition sequences (like HinfI's G^ANTC), cut positions, and site counts — correctly detecting sites that span a circular plasmid's origin, unlike a naive linear scan.
How to use Restriction Sites
- 1Paste or type a DNA sequence in the editor below (or load the example), and check "Circular" if it's a plasmid.
- 2Open the Restriction sites panel — it defaults to unique (single-cut) sites; toggle "Show all sites" for the complete list.
- 3Check any enzyme to mark its cut site directly on the map and see the predicted fragments in the embedded virtual gel.
Frequently asked questions
Which enzymes are included?
A curated set of ~50 commonly used enzymes (EcoRI, BamHI, HindIII, NotI and many more), including some with degenerate recognition sequences.
Are degenerate recognition sequences handled?
Yes. Enzymes with IUPAC codes (e.g. HinfI G^ANTC) are matched correctly using the full ambiguity alphabet.
Can I edit the sequence, not just scan it?
Yes — this is the same SeqStudio editor available at /tools/seqstudio: every keystroke remaps features live, with undo/redo, auto-annotation, GenBank/SnapGene import, GenBank export, and multi-document tabs.