Generate publication-quality circular and linear DNA sequence maps. Annotate restriction sites from 250+ enzymes, open reading frames, custom features, and primer binding sites. SVG export for figures. Data never leaves your browser.
Try it out
Load example sequence mapper data to see the full workflow
When to use
Do not use for
Selecting more than 8-10 enzymes makes circular maps cluttered. For publication figures, choose only the enzymes relevant to your cloning strategy.
SVG exports are vector format and scale to any size without quality loss. Import into Illustrator, Inkscape, or Affinity Designer to adjust labels and styling before submission.
The ORF finder reports all ATG-to-stop regions above the length threshold. It does not predict actual genes (no Shine-Dalgarno analysis, no Kozak context). Use for orientation, not gene annotation.
When entering custom features, use 1-based positions (as in GenBank files). The tool converts internally to 0-based for rendering.
Circular topology renders a ring diagram (standard plasmid map). Linear topology renders a horizontal bar with annotations above and below. Choose based on your construct type.
250+ restriction enzymes from REBASE. ORF detection across all 6 reading frames (ATG to stop codon, configurable minimum length). Feature parsing from GenBank-style notation. Primer binding by exact sequence match on both strands with Wallace/simplified Tm estimate. SVG generation with layered annotations.
Last validated 2026-04-07. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.
ConductScience Restriction Site Sequence Mapper (v1.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/restriction-site-sequence-mapper
Vincze T, Posfai J, Roberts RJ. NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res. 2003. doi:10.1093/nar/gkg526
Roberts RJ et al. REBASE—a database for DNA restriction and modification. Nucleic Acids Res. 2023. doi:10.1093/nar/gkac975
Annotated sequence maps are essential for communicating construct design in molecular biology publications. A well-designed map shows:
• Restriction sites: Where key enzymes cut, critical for cloning strategy • ORFs / CDS: Protein-coding regions with reading frame information • Regulatory elements: Promoters, terminators, origins of replication • Primer binding sites: For PCR verification and sequencing
Circular maps (plasmid maps) are the standard representation for vector constructs. Linear maps are used for PCR products, chromosomal regions, and linearized constructs.
NEBcutter, developed by New England Biolabs, has been the standard online tool for restriction enzyme analysis since 2003. It generates annotated sequence maps showing where restriction enzymes cut a given DNA sequence.
Key features of restriction mapping: • Single-cutter identification: Enzymes that cut exactly once are ideal for linearizing circular DNA • Unique site analysis: Important for inserting DNA at a specific location • Multi-enzyme maps: Show the relative positions of multiple enzyme sites • ORF overlay: Identify potential coding regions in the sequence
For journal submissions, vector maps should be:
• Vector format (SVG/EPS): Journals require 300+ DPI; vector formats scale infinitely • Clearly labeled: Gene names, restriction sites, and key features should be legible • Color-coded: Use distinct colors for different feature types • Properly oriented: Convention places the origin of replication at 12 o’clock • Size-annotated: Include the total construct size in bp/kb
Export the SVG from this tool and refine labels in a vector editor (Illustrator, Inkscape) for final publication.
