💡 Quick Summary

Restriction Summary scans one or more DNA sequences against the full standard set of restriction enzymes and reports, for each enzyme, how many times it cuts and the exact cut positions. Results are colour-coded by cut count — non-cutters are dimmed, single-cutters are highlighted green (useful for linearising a plasmid), double-cutters are highlighted blue (useful for excising a fragment), and higher-frequency cutters are shown in orange.

📋 How to Use

Paste one or more DNA sequences (raw or FASTA) into the text area.
Select the molecule topology: linear (default) or circular.
Click Submit. A table is shown for each sequence listing every enzyme, its cut count, and the 1-based positions of each cut.
Use the Show filter above the table to limit the view to a specific cut-count category (e.g. "Cuts once" to find linearising enzymes).
Click Load Example to analyse a sample sequence.
Use Copy All to copy the plain-text report to your clipboard.

🧮 Formulas & Logic

Cut position (linear)

matchEnd − cutDistance, where matchEnd is the regex lastIndex and cutDistance is the number of bases from the end of the recognition site to the cut. Reported as a 1-based position after which the cut occurs.

Cut position (circular)

Same calculation applied to an extended sequence (±50 bp wraparound). Positions outside the original length are discarded.

📊 Result Interpretation

Non-cutters (0)

Dimmed rows — the enzyme has no recognition site in the sequence.

Single-cutters (1)

Green rows — the enzyme cuts exactly once. Useful for linearising a circular molecule without fragmenting it.

Double-cutters (2)

Blue rows — the enzyme cuts twice, excising a single internal fragment.

Multiple cutters (3+)

Orange rows — the enzyme cuts three or more times; usually not useful for cloning but can be diagnostic.

Cut position meaning

Position p means the cut occurs after the p-th base. The left fragment ends at base p; the right fragment starts at base p+1.

🔬 Applications

Quickly identifying which enzymes cut (or do not cut) a cloning vector or insert
Finding single-cutting enzymes to linearise a plasmid for transfection
Selecting a pair of enzymes that excise a specific fragment
Checking that a given restriction site is unique before cloning
Comparing restriction patterns of two similar sequences to identify diagnostic enzymes

⚠️ Common Mistakes & Warnings

Sequence-based only

This is a purely sequence-based virtual digest. Methylation-sensitive enzymes (e.g. ClaI blocked by Dam methylation) may show more sites in silico than in a real experiment.

Isoschizomers not merged

Enzymes that share an identical recognition sequence (e.g. SacI and SstI) each appear as separate rows. If both show one cut, only one enzyme is needed — picking either will cut at the same position.

❓ Frequently Asked Questions

How is a circular molecule handled?

For a circular molecule the sequence is virtually extended with 50 bp from the end prepended and 50 bp from the start appended before searching. Only cut positions that fall within the original sequence length are recorded. This ensures recognition sites that span the origin of the circular molecule are detected correctly.

What does "position 0" mean?

A reported position of 0 means the cut falls at the very beginning of the sequence — before the first base. This can occur with circular topology when the recognition site spans the origin.

Why do some enzymes appear more than once?

Some recognition sequences are shared by multiple enzyme names (isoschizomers). For example, SacI and SstI both recognise GAGCTC. Each is listed separately so you can choose the enzyme available in your lab.