Free AI-Assisted
Restriction Enzyme Mapper
Find restriction cut sites with Dam/Dcm methylation warnings, circular plasmid maps, virtual gel previews, and SVG export—no account needed. Built-in AI agent assistant support.
Need help with bioinfo analysis? See our bioinformatics services.
Key facts
| Fact | Value |
|---|---|
| Inputs | Plain DNA or FASTA sequence, optional sequence name label |
| Sequence limits | 20 bp minimum, 500,000 bp maximum; IUPAC ambiguous base support |
| Topology | Circular (default) or linear plasmid map rendering |
| Enzyme database | ~70 common cloning restriction enzymes (REBASE subset) |
| Cut frequency filter | 1 cut (single-cutters, default), 2 cuts, or all cuts |
| Feature filters | Hide sites < 6 bp (default ON), hide redundant isoschizomers (default ON) |
| Methylation flags | Dam (GATC), Dcm (CCWGG), and CpG (CG) overlap warnings with unblocked alternatives |
| Map & gel views | Interactive SVG circular/linear map, virtual gel with 1 kb Plus ladder (100–10,000 bp) |
| Output & export | Vector SVG map, 2× PNG raster figure, TSV fragment size table (clipboard) |
| Runs in browser | Yes — 100% client-side, zero server uploads |
| Account required | No |
What it does
Planning a restriction digest traditionally requires switching between server-dependent web tools that suffer latency, obscure Dam/Dcm methylation warnings behind option menus, and fail to export clean figures. Restriction Enzyme Mapper eliminates server dependency by evaluating sequences up to 500,000 bp against a local database of ~70 canonical cloning enzymes. Input validation automatically parses FASTA headers and flags non-IUPAC characters inline, allowing researchers to paste sequences directly from GenBank or bench notes without manual cleanup.
The tool organizes matching restriction enzymes into collapsible panels based on overhang type—5′ overhang, 3′ overhang, or blunt ends—so you can quickly identify compatible sticky ends for directional cloning. When a recognition site overlaps Dam (GATC), Dcm (CCWGG), or CpG methylation motifs, the tool marks the enzyme row in red and suggests unblocked commercial alternatives (such as NheI when XbaI is Dam-blocked). Selecting enzymes populates cut positions on the interactive circular or linear plasmid map and updates a virtual gel lane against a 1 kb Plus DNA ladder (100 bp to 10,000 bp). You can export publication-grade SVG vector maps titled with your sequence label, download 2× PNG figures for slides, or copy a TSV fragment table directly to your clipboard.
Why researchers use it
- Analyze plasmid restriction sites instantly without server latency or data uploads
- Detect Dam and Dcm methylation overlap warnings before executing bench digests
- Filter single-cutters in one click to identify unique restriction cloning sites
- Group enzymes by 5′, 3′, or blunt overhangs for compatible-end ligation planning
- Preview digestion fragment bands on a virtual gel against a 1 kb ladder
- Export vector SVG maps and TSV fragment tables for notebooks and manuscripts
Best for
- Single-cutter screening on newly synthesized or isolated plasmid vectors
- Troubleshooting incomplete digests caused by Dam or Dcm bacterial methylation
- Selecting compatible sticky-end restriction pairs for directional insert cloning
- Verifying expected fragment sizes against agarose gel electrophoresis runs
- Generating circular plasmid map figures titled with sequence names for publications
When to use this vs alternatives
Choose Restriction Enzyme Mapper when you need fast, private single-cutter screening and exportable plasmid maps without server lag or paid licenses. For checking PCR primer binding and secondary structure, use Oligo QC Instant. To calculate vector-to-insert ligation ratios after choosing your enzymes, open the Ligation Insert Ratio Calculator. Server tools like NEBcutter remain suitable for whole-genome searches requiring rare or non-commercial enzymes.
What makes it different
Restriction Enzyme Mapper combines client-side processing speed, explicit Dam/Dcm methylation warnings, compatible-end overhang grouping, virtual gel simulation, and free vector SVG export in a single tab. Unlike server-based cutters or commercial desktop suites, it requires no login, subscription fees, or data uploads.
Bench researchers switch to Restriction Enzyme Mapper to avoid digest failures caused by overlooked Dam/Dcm methylation and to eliminate tedious server round-trips. Traditional web tools delay workflow when servers drop connections, while commercial desktop software requires costly licenses per seat. Restriction Enzyme Mapper provides sub-second analysis, instant single-cutter filtering, interactive gel simulation, and free SVG figure export directly in your browser. The built-in assistant helps interpret complex digestion warnings, while external AI workflows can connect via MCP.
How to get started
- Open the RE Finder tab in your browser workspace.
- Paste plain DNA text or a FASTA sequence into the Sequence Input field (a default pUC19 sequence is pre-loaded).
- Enter an optional label in the Sequence Name field and select your plasmid Topology (Circular or Linear).
- Set the Cut Frequency filter (default is 1 for single-cutters) and toggle site length or isoschizomer display options.
- Inspect the interactive plasmid map and click enzyme names in the overhang groups to highlight cut sites and display fragment bands on the Virtual Gel.
- Click Export SVG or Export PNG to save vector/raster figures, or click Copy Fragment Table to copy TSV data to your clipboard.
Frequently asked questions
Is my DNA sequence uploaded to a remote server during restriction mapping?
Why are certain restriction enzymes highlighted in red with methylation warnings?
How does the Cut Frequency filter work, and what is single-cutter screening?
What image formats are available for exporting plasmid maps and figures?
Can I use ChatGPT, Cursor, or another AI agent with Restriction Enzyme Mapper?
Client source code & registry
Last updated . Pepkio builds free lab calculators alongside bioinformatics CRO services.