Free Restriction Enzyme Finder
Scan any DNA sequence for restriction enzyme cut sites, compute fragment sizes, and identify sticky or blunt ends from a built-in database of common enzymes. No login, no queue, no limits.
VigyanLLM's restriction enzyme finder scans a DNA sequence and reports every recognition site, the exact cut positions, the resulting fragment sizes, and the type of ends each enzyme produces. Paste a sequence, choose one enzyme or run a full restriction digest, and the tool returns a complete restriction map.
| Enzyme | Recognition Site | Cut (5'→3') | Ends |
|---|---|---|---|
| EcoRI | GAATTC | G^AATTC | Sticky (5') |
| BamHI | GGATCC | G^GATCC | Sticky (5') |
| HindIII | AAGCTT | A^AGCTT | Sticky (5') |
| NotI | GCGGCCGC | GC^GGCCGC | Sticky (5') |
| XbaI | TCTAGA | T^CTAGA | Sticky (5') |
| SalI | GTCGAC | G^TCGAC | Sticky (5') |
| SmaI | CCCGGG | CCC^GGG | Blunt |
| EcoRV | GATATC | GAT^ATC | Blunt |
Choose "All enzymes" for a complete restriction map of your sequence, or pick a single enzyme. The text box filters the 39-enzyme database.
Results will appear here
| Enzyme | Recognition Site | Position(s) | Cut Pattern | Ends | Fragment sizes |
|---|
| Fragment | Length |
|---|
How Restriction Enzyme Mapping Works
Restriction enzymes (Type II endonucleases) recognize short, specific, usually palindromic double-stranded DNA sequences of 4–8 base pairs and cleave them at a precise position. The tool compares every position in your sequence against each enzyme's recognition site, so every match identifies one cut position on the 5 prime strand. Because recognition sites are palindromic, a match implies the equivalent cut exists on the antiparallel strand, so a single forward scan builds the complete map. After collecting all cut coordinates, the sequence is split: the first fragment spans base 1 to the first cut, each internal fragment spans two adjacent cuts, and the final fragment runs from the last cut to the end. The result is a set of fragment sizes whose lengths always sum to the total sequence length.
Common Use Cases
- Cloning: Identify enzymes that cut your insert once and in the vector's multiple cloning site to generate compatible, directional sticky ends
- RFLP analysis: Predict the fragment size distributions used to distinguish alleles, strains, or genotypes on a gel
- Plasmid verification: Confirm construct identity by comparing predicted digest fragments with the pattern seen after gel electrophoresis
- Fragment-based genotyping: Choose a set of enzymes whose combined cut pattern yields a unique fingerprint for a target locus
About VigyanLLM
VigyanLLM is India's first sovereign, on-premises biomedical AI platform. Beyond sequence analysis, VigyanLLM provides autonomous primer design with 24-parameter validation, CRISPR guide RNA analysis, GPU-accelerated molecular docking, BLAST, and MSA — all deployed on your hardware with zero data leakage. Free for Indian universities.
Frequently Asked Questions About Restriction Enzyme Finder
Everything you need to know about restriction mapping with this tool
What is a restriction enzyme cut site?
A restriction enzyme cut site (recognition site) is a short, specific double-stranded DNA sequence, usually 4–8 base pairs long, that a restriction endonuclease recognizes and binds to before cutting. Each enzyme cuts at a precise position within that sequence. For example, EcoRI recognizes the palindrome GAATTC and cuts between the G and the A on the forward strand, leaving a 4-base 5 prime overhang. Most Type II sites are palindromic, meaning they read the same on both strands in the 5 prime to 3 prime direction, which permits a single forward-strand scan to build the complete map.
How is the restriction map calculated from a DNA sequence?
The tool scans the input sequence in the 5 prime to 3 prime direction and compares every substring against each enzyme's recognition code (IUPAC). Each match produces one cut position computed as the recognition-site start index plus the enzyme's cut offset. All cut positions are then sorted, and fragment lengths are derived by subtracting consecutive cut coordinates: the first fragment spans base 1 to the first cut, each internal fragment spans two adjacent cuts, and the last fragment runs from the final cut to the end of the sequence. The fragment lengths always sum to the total sequence length, which also serves as a built-in sanity check.
What is the difference between sticky ends and blunt ends?
Blunt ends are produced when the enzyme cuts both strands at the same position, leaving two flush double-stranded ends (for example SmaI or EcoRV). Sticky (cohesive) ends occur when the two strands are cut at different positions, leaving a short single-stranded overhang of 1–4 bases: a 5 prime overhang leaves the unpaired tail on the 5 prime strand (EcoRI, BamHI, NotI), while a 3 prime overhang leaves it on the 3 prime strand (KpnI, ApaI, PstI). Sticky ends are preferred for cloning because complementary overhangs anneal spontaneously and ligate at high efficiency; blunt ends ligate more slowly and can join any two blunt molecules.
Can I find restriction sites for cloning into a specific vector?
Yes — this is one of the most common uses of the tool. Paste both your insert and the multiple cloning sequence (MCS) of the vector into the finder, then look for enzymes that cut once in your insert at a convenient position and also cut in the MCS with compatible sticky ends. Six-base cutters such as EcoRI, BamHI, HindIII and XbaI appear rarely in random DNA (about once per 4,096 bp) and are good candidates. Avoid enzymes whose site appears more than once inside your insert, since that would cleave the insert internally, and confirm no unwanted sites fall inside essential genes such as the antibiotic resistance marker.
Are restriction enzymes and their sites accurate for real lab experiments?
The recognition sites and cut coordinates in this tool follow the consensus data published for Type II restriction enzymes and match the information in REBASE, the international reference database. It is accurate for predicting which sites exist and roughly where they fall. However, real digests can differ in practice: Dam/Dcm methylation in E. coli can block enzymes such as BamHI, EcoRI and HindIII; star activity under high glycerol or prolonged incubation can cause EcoRI to cut non-canonical sites; and isoschizomers or sites in unusual sequence context may cut poorly. Always confirm fragment sizes on a gel and check your strain's methylation status before relying on a predicted digest for a critical cloning step.