PlasMapper draws an annotated plasmid map from a DNA sequence — automatically detecting and labelling features such as ORFs, restriction sites, promoters, origins, selectable markers and tags. Paste your sequence into the official PlasMapper tool embedded below, then use the guide to read and refine your map.
Open PlasMapper in a new tab ↗ (recommended on small screens).
What PlasMapper does
Give it a plasmid sequence (raw, FASTA or GenBank) and PlasMapper produces a circular map with the common features of an expression or cloning vector annotated automatically. It is the fast way to visualise a construct, document a plasmid for a notebook or publication, and spot the restriction sites and elements you need before designing a cloning step.
How to use it
- Paste your plasmid sequence and set the topology to circular.
- Run the annotation — PlasMapper scans for ORFs, restriction sites, regulatory elements and common vector features.
- Review and export the map; download it as an image or vector file for your records or figures.
What gets annotated
- ORFs and coding regions
- Restriction sites (single cutters are the most useful for cloning — cross-check with a dedicated tool such as NEBcutter)
- Promoters, terminators and origins of replication
- Selectable markers (antibiotic resistance) and common tags
Frequently asked questions
What input does PlasMapper accept?
A DNA sequence as raw text, FASTA or GenBank format. Set the molecule to circular for a plasmid.
Can I export the map?
Yes — PlasMapper lets you download the generated map as an image/vector file suitable for lab notebooks and figures.
Does it find restriction sites?
Yes, it annotates restriction sites among other features. For a focused restriction analysis (single cutters, fragment sizes), pair it with NEBcutter.
Related guide: Restriction enzyme cloning: a step-by-step guide →
