Restriction Mapper and Site Analyzer Help

Useful Checks

• Use this before ligation setup to confirm enzyme sites and fragment sizes, then use the Ligation Calculator for insert-to-vector mass calculations.
• The current sequence can be opened in Primer Designer or Primer Binding Checker, connecting restriction-site analysis with primer design and binding checks.

How To Use

1. Paste or upload the sequence.
2. The sequence limit is 100,000 bases. A transfer from a tool with a larger limit is rejected if it exceeds this limit; select a shorter region or use a tool that accepts the complete sequence.
3. Check the DNA topology. An explicit circular or linear declaration in a valid GenBank LOCUS line is applied automatically until you choose a topology manually. Clear resets that manual choice.
4. Enter enzyme names only if you want to focus the scan.
5. Choose an enzyme group or result filter if needed.
6. Click Analyze restriction sites.
7. Editing the sequence or uploading a new file clears old results. Changing topology or digest enzymes can recalculate the existing analysis; map display controls do not require a new scan.
8. Click enzyme badges or map labels to add or remove enzymes from the digest preview. Select multiple enzymes for a combined digest. Show all detected sites clears the selection and restores the full map.

Understanding The Results

• The table shows enzyme names, recognition-site counts, and 1-based recognition ranges.
• The linear or circular map marks recognition-site start positions; circular mode also detects sites crossing base 1. Circular labels may move apart for readability; follow each leader line to its site.
• Dense maps show a spaced subset of site labels. Hidden labels do not mean sites were omitted from analysis. Use the site table and downloaded positions for the retained results, and check any stated display or storage limits. On the circular map, hover an enzyme to show its site labels.
• The digest preview uses manufacturer cleavage offsets for the selected enzymes. Lengths count top-strand bases between cuts, including overhang bases; the cut summary reports both strand boundaries and cohesive-end sequences.
• When different enzymes leave compatible cohesive ends, the digest selection warns that those ends can ligate. This concerns DNA-end compatibility, not whether the enzymes share suitable reaction conditions.
• The virtual gel estimates the fragment pattern. A dashed band marks the full-length linear reference and is omitted when the only fragment spans the whole input. One cut linearizes a circular plasmid; an uncut circular plasmid is not shown as a linear fragment band.
• The highlighted sequence shows sites in sequence context.
• Copy summary preserves the selected digest, site counts, positions, and predicted fragments.

Read the virtual gel

Band centres follow the logarithmic size axis. Nearby fragments can overlap in this schematic; they are not spread apart to suggest experimental separation. Use the fragment table for exact sizes and positions.

Accepted Input Formats

• Raw DNA sequence.
• FASTA.
• GenBank text with an ORIGIN sequence section. Feature annotations, including ori/origin-of-replication annotations, are ignored.
• Multiple FASTA records are concatenated for analysis and may create artificial junction sites. Analyze separate records one at a time.
• IUPAC-degenerate enzyme recognition sites and reverse-complement site matching are supported.
• .dna / SnapGene binary files are not supported. Export as FASTA or GenBank.

Assumptions And Limitations

• The tool scans its built-in enzyme set, not every known enzyme. It does not predict methylation sensitivity, star activity, partial digestion or buffer compatibility.
• Type IIS cuts use the surrounding input sequence. Recognition sites without a complete cleavage region are excluded with a warning. Overlapping cleavage regions suppress the fragment and gel predictions.
• Compatible-end warnings compare resolved ends, including variable Type IIS and degenerate-site ends when their sequence is available. A recognition-site match does not guarantee enzyme activity, particularly near DNA ends. Check methylation sensitivity, buffer compatibility and incubation conditions with the supplier.
• The virtual gel is a planning schematic. Top- and bottom-strand lengths may differ at staggered ends; fragment spans are not a prediction of electrophoretic mobility.
• The browser tool accepts sequence files smaller than 2 MB and sequences up to 100,000 bp.

Example

Use this result with other tools

Direct destinations: Open in Primer Designer sends the validated input sequence and selected DNA topology to Primer Designer so you can design primers around a region or cloning junction. Open in Primer Binding Checker sends the same template and topology to Primer Binding Checker so you can enter and test an existing pair. The selected enzymes, digest fragments and enzyme filters are not transferred.

Receiving a template: Primer Designer and Binding Checker can open the sequence here. Confirm the imported topology, choose the enzyme group and click Analyze restriction sites.

Manual follow-up: use the selected vector/insert fragment lengths in Ligation Calculator to calculate an insert mass for restriction-and-ligation cloning. Copy or export the exact retained DNA pieces into Assembly PCR Primer Designer or Gibson Assembly Primer Designer for overlap joining. Those designers accept an already-linear blunt backbone or PCR opening; a restriction-site coordinate alone does not describe staggered ends.

Correcting highlighted input

When the main action rejects pasted sequence text, unsupported characters are highlighted in the field and the error message explains the problem. Correct the marked characters using the alphabet allowed by this tool, then run it again. The highlights update as you edit. A malformed FASTA or GenBank record may require a structural correction even when no individual character is marked.