Plasmid Designer
Upload a GenBank or FASTA file to draw a circular plasmid map, annotate restriction enzyme sites, and export the map as PNG or SVG.
Learn more
What it does
The Plasmid Designer is a browser-based tool that turns a GenBank or FASTA sequence into a circular plasmid map. It annotates biological features, finds restriction enzyme cut sites from a built-in database of common enzymes, and exports the finished map as PNG or SVG. Molecular biologists use it to plan cloning, verify constructs, and produce publication-ready figures without desktop software.
How it works
The tool parses the sequence and its feature table and lays features on a circular coordinate system measured in base pairs. It scans the sequence against restriction enzyme recognition sites; a single-cutter with one site linearizes the plasmid into one fragment, while multiple cutters fragment it, with each fragment size equal to the distance between adjacent cut positions along the circle. Sites can be filtered to common enzymes or single-cutters to simplify the cloning strategy.
Worked example
Load the built-in pUC19 sample, which is 2686 base pairs. Tick EcoRI and BamHI. The map shows each gene and feature as a colored arc and the two enzyme sites as red ticks at their base-pair positions. A single EcoRI digest yields one 2686 base pair linear fragment, while a double digest with BamHI splits pUC19 into two fragments whose sizes equal the distances between the two cut sites around the circle.
When to use it
A researcher uses it to find a unique restriction site for inserting a gene into a multiple cloning site, to plan a double-digest cloning strategy and predict fragment sizes for a gel, and to generate an annotated map for a methods section or lab notebook.
FAQ
- How do I design a plasmid map?
- Upload a GenBank dot gb or FASTA dot fasta file, or load the pUC19 sample. The tool draws a circular map with annotated features and restriction sites; zoom, rotate, and click any site to inspect the cut position and fragment sizes, then export as PNG or SVG.
- How do I find restriction enzyme sites in my plasmid?
- After loading the sequence, tick enzymes in the left panel. The tool scans the sequence against a built-in database of common enzymes and marks each cut site as a red tick on the circular map, with positions and fragment sizes shown on click.
- What is a single-cut enzyme and why does it matter?
- A single-cut enzyme has exactly one recognition site in your plasmid, so a digest linearizes the circular DNA into one fragment. Single cutters are useful for confirming topology or inserting a fragment at a unique site; the Single cut filter lists them quickly.
- How do I export a plasmid map as PNG or SVG?
- After loading and annotating the plasmid, click the PNG or SVG button to download the map. SVG keeps vector quality for publication figures, while PNG is convenient for lab notebooks and presentations.