Tools that run on your own sequences
Free molecular biology tools in the browser: cloning workspace, PCR primer design, alignment of up to 200 sequences, restriction digests and oligo Tm.
Restriction digest simulator
Simulate a restriction digest: REBASE enzyme sets, Dam/Dcm/EcoKI methylation, cut sites on circular and linear maps, and fragments sent to a gel.
Free · no install
Oligo Tm calculator
Oligo melting temperature by nearest-neighbour thermodynamics, with GC content and duplex Tm for annealed pairs, plus a compatible-overhang lookup.
Free · no install
PCR primer design tool
Design PCR primers in the browser: pairs ranked on Tm, GC, 3′ clamp, hairpins, dimers and binding sites, plus a 5′ overhang builder for sites and tags..
Free · no install
Multiple sequence alignment tool
Align up to 200 DNA, RNA or protein sequences in the browser, with consensus, conservation, identity matrix and tree.
Free · no install
Cloning workspace
Build a cloning strategy as a node graph: 16 operations from digest and PCR to Gibson, Golden Gate, Gateway and CRISPR-HDR, saved as OpenCloning JSON..
Free · no install
Plasmid map maker
Make an annotated plasmid map from GenBank, FASTA or SnapGene .dna: circular and linear maps in sync, exported as SVG, PNG, PDF or Word.
Gibson Assembly designer
Design a Gibson Assembly in the browser: pick fragments and Talindrew sets the overlaps, tunes their Tm, writes the primers and checks the design.
Golden Gate Assembly designer
Golden Gate design in the browser: Type IIS enzymes, 4 nt fusion sites chosen to minimise scars, overhang and methylation checks, and MoClo kits.
Looking for a standalone calculator instead? The biomath calculators run without an account and show their formula, a worked example and the reference they are checked against.
Start with a worked example
Free to start. Runs in any modern browser, nothing to install.