Restriction Map

Restriction Map
Map restriction enzyme cut sites on a DNA sequence with optional translation
DNA Sequence

Raw DNA sequence or one or more FASTA sequences. Non-letter characters are removed automatically. Input limit: 100,000,000 characters.

Options
💡 Quick Summary

Restriction Map accepts a DNA sequence and returns a textual map showing the positions of restriction endonuclease cut sites. The complementary strand and optional translation are shown for the reading frame you specify. Use the output as a reference when planning cloning strategies. Supports the full IUPAC alphabet and multiple genetic codes.

📋 How to Use
  1. Paste a raw DNA sequence or one or more FASTA sequences into the textarea. Input limit: 100,000,000 characters.
  2. Set bases per line — how many bases to display on each row (30, 45, 60, 75, 90, or 105).
  3. Choose a reading frame: All three shows all three forward reading frames simultaneously; Frame 1/2/3 shows a single frame above the sequence; Uppercase only translates only uppercase runs (useful for GenBank exon/intron sequences); None suppresses translation.
  4. Select the genetic code used for translation (default: Standard).
  5. Set topology to Circular to detect sites that wrap around the origin of a circular molecule.
  6. Choose Colour or Black & white output.
  7. Click Run. Enzyme names are printed above the sequence at their cut positions, colour-coded green (1 cut) or orange (2 cuts). The Restriction Site Summary table below the map lists all cutting enzymes with positions. Use Copy to copy the plain-text map.
🧮 Formulas & Logic
Green label — cuts once
The enzyme cuts the sequence exactly once. Ideal for linearising circular DNA or directional cloning.
Orange label — cuts twice
The enzyme cuts the sequence twice. Useful when excising a defined fragment between two sites.
Plain label — cuts 3+
The enzyme cuts three or more times. Usually not suitable for simple cloning steps.
📊 Result Interpretation
Label position

Each enzyme label is horizontally aligned above the first base of its recognition site in the sequence row.

Position number

The number appended to each enzyme name is 1-based and indicates the first base of the recognition site.

Ruler row

The row of numbers between the sense and antisense strands shows absolute position every 10 bases.

Complement row

The lower strand shows the complementary (antisense) sequence written 3′→5′ beneath the sense strand.

Translation rows

Amino acids are placed at the first base of each codon. Stop codons appear as *. Rows appear above the sense strand.

🔬 Applications
  • Planning restriction cloning strategies for plasmid or vector construction
  • Identifying unique restriction sites for linearising a circular DNA molecule
  • Confirming the restriction pattern of a PCR product or synthetic gene before cloning
  • Generating annotated sequence figures showing cut sites and reading frames for publications
  • Checking open reading frames and stop codons in the context of known restriction sites
⚠️ Common Mistakes & Warnings
Non-IUPAC characters are stripped

Numbers, spaces, and non-letter characters are removed before analysis. Only IUPAC nucleotide letters (A, T, G, C, R, Y, K, M, S, W, B, D, H, V, N, U) are retained.

Only standard restriction enzymes are included

The built-in enzyme set covers the most common commercially available enzymes. Rare-cutter or custom enzymes are not included.

Circular topology look-ahead is limited to 50 bases

For circular molecules, only recognition sites within a 50-base window at the sequence junction are detected. Recognition sequences longer than 50 bases that span the origin may be missed.

❓ Frequently Asked Questions

How do I identify the best enzyme for cloning?
Look for green-labelled enzymes in the map — they cut exactly once. A pair of green enzymes flanking your insert gives directional cloning without releasing unwanted internal fragments. Check the summary table to confirm positions.
Why are some enzymes absent from the summary table?
Only enzymes that cut at least once in the input sequence are listed. Enzymes with zero matches are omitted. The summary is sorted by cut frequency so unique cutters appear at the top.
What does the "Uppercase only" reading frame do?
It translates only runs of consecutive uppercase letters, treating lowercase characters as non-coding gaps. This is useful for sequences exported from tools like GenBank Feature Extractor where exons are uppercase and introns are lowercase.
How does circular topology change the results?
When Circular is selected, the tool also searches a 50-base window at the sequence junction for recognition sites spanning the origin. Sites near the 3′ end that continue into the 5′ beginning are detected as a single cut event.
Restriction Map — logic ported from the Sequence Manipulation Suite (Paul Stothard, University of Alberta).