Tools that run on your own sequences
Free molecular biology tools that run in the browser on your own sequences: design PCR primers, align up to 200 sequences, simulate a restriction digest and calculate oligo melting temperatures. Each page explains the method, the defaults and where they come from.
Restriction digest simulator
Simulate a restriction digest in the browser: enzyme sets drawn from REBASE, Dam/Dcm/EcoKI methylation sensitivity, cut sites mapped onto circular and linear views, and fragment sizes fed straight into a gel simulation.
Free · no install
Oligo Tm calculator
Calculate oligo melting temperature with nearest-neighbour thermodynamics, plus GC content, length and duplex Tm for annealed pairs.
Free · no install
PCR primer design tool
Design PCR primers in the browser: ranked primer pairs scored on nearest-neighbour Tm, GC content, 3′ clamp, hairpins, self- and cross-dimers and template binding sites, with a 5′ overhang builder for restriction sites, tags and Gibson arms.
Free · no install
Multiple sequence alignment tool
Align up to 200 DNA, RNA or protein sequences in the browser: progressive alignment with affine gaps and BLOSUM62, consensus, conservation, identity matrix and tree, with MAFFT, MUSCLE or Clustal Omega when available.
Free · no install
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.