Virtual Gel — Restriction Digest Simulator
Predict restriction fragments and see the simulated agarose gel with a ladder.
A standalone restriction digest simulator: paste a linear fragment or a circular plasmid, click one enzyme (or two for a double digest) from the 18 on offer, and the virtual gel draws the predicted bands beside a 1 kb, 1 kb Plus or 100 bp ladder. Fragment sizes are listed next to the agarose gel image, which downloads as SVG, PNG or PDF.
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Fragments are predicted from the recognition sites of the selected enzymes; band positions use a log-size migration model against the chosen ladder. Uncut circular DNA runs as a single (super)coiled species. This is a prediction — real migration depends on gel %, voltage and conformation.
Screening clones? Pick the digest that tells them apart
The gel above shows what the right plasmid cuts into. A diagnostic digest also has to look different for everything else you might have picked — empty vector, an insert the wrong way round, a misassembly. This digests each of those as well and ranks enzymes by whether the bands that actually resolve on your gel separate the right clone from every wrong one.
Planned for the construct in the gel form above — paste it there first.
Searching all 49 curated enzymes.
Design, edit, and verify complete constructsSeqStudio combines sequence editing and annotation, plasmid maps, primer/cloning/CRISPR design, Sanger verification, and GenBank/SnapGene files in one workspace.
How to use the Virtual Gel tool
- 1Paste a plasmid or DNA fragment into the DNA sequence (raw or FASTA) box, or click Load example.
- 2Tick Circular (plasmid) if it is a closed circle, and pick your Ladder: 1 kb, 1 kb Plus or 100 bp.
- 3Click enzyme buttons (EcoRI, BamHI, HindIII and 15 more) to add or remove them from the digest; selected ones turn green, and two or more give a double digest.
- 4Read the Fragments, Cuts and Largest stats, the Cutters line, the fragment size table and the simulated gel, then download the figure from the Figure button as SVG, PNG or PDF, or copy a share link.
Frequently asked questions
How are the band positions determined?
Fragment sizes come from the recognition sites of the enzymes you select. Each band is placed by a log-size migration model spanning your fragments and the ladder you picked (1 kb, 1 kb Plus or 100 bp), so larger fragments migrate less. It is a prediction; real migration also depends on gel percentage, voltage and DNA conformation.
Does it handle double digests and circular plasmids?
Yes. Check multiple enzymes for a double (or triple) digest, and toggle Circular for a plasmid — fragments are computed around the circle, correctly handling a recognition site that spans the origin. Uncut circular DNA runs as a single band.
Can I export the gel image?
Yes. The Figure button above the gel downloads it as SVG, PNG or PDF, and the same menu has a Watermark tick that turns off the seqbench.com credit for publication-quality figures. The fragment sizes are also listed in the table next to the gel so you can copy them straight out.