Molecular Cloning
4 toolsGibson Assembly designer
Design homology-arm primers for seamless multi-fragment Gibson Assembly. Supports multiple inserts, single and circular vectors, with configurable homology length and Tm.
Restriction cloning designer
Identify unique-cutter sites in your vector, design directional cloning primers with restriction sites and 5' clamps, and detect internal sites in the insert automatically.
Site-directed mutagenesis
Translate your sequence, click a residue, pick the target amino acid, and get inverse-PCR primers with the optimal E. coli codon — fewest nucleotide changes, highest usage frequency.
CDS Finder
Find the exact DNA stretch encoding a protein across all six reading frames, ready for truncated-construct primer design.
Protein Expression
Coming soonConstruct optimizer
Tag and vector selector for recombinant protein expression — based on target properties, expression host, and downstream application.
Protein Analysis
3 toolsDSF Analysis
Paste raw fluorescence data from a spreadsheet, normalize the signal, calculate melting temperatures from the derivative minimum, and export publication-ready results.
Gel Analyzer
Measure bands in SDS-PAGE and agarose gel images, calibrate against a marker, and export annotated figures and results.
Structure Editor
Inspect, recolor, edit, and export PDB or mmCIF structures in an interactive 3D viewer without uploading files.
Citing these tools
Zenodo · DOIIf these tools help your work, a citation helps ours
These tools are free to use and always will be. They are built and maintained in the open, and citations are the main way that work stays visible and fundable. If you used any of them to design primers for a published experiment, we would be grateful if you cited the archived release — no permission or acknowledgement is required to use them either way.
S Godoy, A. (2026). Three web-based, client-side primer design tools for Gibson Assembly, restriction cloning, and site-directed mutagenesis. Zenodo. https://doi.org/10.5281/zenodo.22798744