Cloning
Restriction Digest
Choose enzymes and see what they do to the sequence: every recognition site on both strands, the fragments a digest produces, and those fragments as bands on a virtual gel. Circular sequences are cut as circles, so a fragment that spans the origin has the length it would really have.
Phage λ plus five plasmids from 2.2 to 7.3 kb: run the λ/HindIII marker you build from its own sequence, beside real digests at an adjustable agarose percentage
What it does
- 01Recognition sites from the bundled REBASE dataset, matched with full IUPAC degeneracy
- 02Circular-aware cutting, so an origin-spanning fragment gets its true length
- 03Fragment table with lengths and ends
- 04Multi-lane virtual gel at an adjustable agarose percentage, against real molecular-weight ladders
- 05Single-cutter filtering, for choosing an insertion site
- 06Fragments opened as their own sequences, or sent to the gel bench
What it runs on
Digestion runs on the pydna port; gel migration uses a published log-linear mobility law, golden-validated rather than fitted by eye. The panel runs on @ports/enzymes, @ports/gel, @ports/rebase.
Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.
Questions
- Does it handle degenerate recognition sequences?
- Yes. Sites are matched with full IUPAC degeneracy, so an enzyme whose site contains N, R, Y or W matches every sequence it really matches.
- Can I see the digest as a gel?
- Yes. Fragments can be rendered as bands on a multi-lane virtual gel at an adjustable agarose percentage, next to real molecular-weight ladders.
Also searched as
restriction digest online · virtual gel electrophoresis · restriction enzyme site finder · plasmid digest simulator · REBASE enzyme search · restriction map tool · agarose gel simulator · double digest calculator · NEBcutter alternative · restriction map online free · double digest fragment sizes · which enzymes cut my plasmid · plan a cloning digest