Design DNA and mRNA
on your own machine.
Nucleora turns reference genomes into an interactive workbench: search a real antigen, codon-optimize it for the animal you're targeting, assemble a complete mRNA construct, fold the RNA, simulate the manufacturing run, and price out the order — all in one local-first window, with 530+ tools underneath when you need them.
Free while in development · macOS & Windows · your sequences stay on your computer
The whole workflow, one window
No stitching together five web tools and a spreadsheet. Nucleora keeps the design, the analysis, and the numbers in the same place — real BioPython, real ViennaRNA folding, real codon-usage tables, computed on your machine.
Codon optimization
Re-code a protein for any host — including elephants, okapi, and other conservation species with real or clade-proxy codon tables — with a live before/after readout.
mRNA construct design
Assemble T7 promoter, 5′UTR, Kozak, signal peptide, antigen ORF, 3′UTR and poly(A) into a therapeutic-style mRNA, with every part's provenance cited.
RNA folding
Fold with the ViennaRNA engine to see secondary structure, minimum free energy, and dsRNA/hairpin immunogenicity risk — computed locally.
IVT simulation & manufacture
Walk the construct through an in-vitro-transcription run, get a graded manufacturability report, then estimate yield, kinetics, and an itemized order form.
Cloning & primers
Restriction mapping, Gibson and Golden Gate assembly, and primer design via primer3 — with a built-in fallback where primer3 has no prebuilt wheel.
Lab bench, in silico
Virtual agarose gels, in-silico PCR, peptide property calculators, and pairwise/multiple alignment — the everyday bench assays, simulated.
Built for the animals that don't have a codon table yet
Codon choice has to match the animal being dosed. Nucleora ships real codon tables built from NCBI RefSeq coding sequences for African elephant, Asian elephant, and cattle — and where a species like okapi or bongo has almost no sequenced genes, it optimizes using a documented, clade-anchored proxy instead of pretending the data exists.
Local-first, and honest about it
What Nucleora is
- A design workbench for DNA and mRNA built on public reference genomes.
- Local-first — your sequences are processed on your machine, not uploaded to a server.
- Method-transparent — every number traces to a named, published algorithm.
- Cross-platform — the same app on macOS and Windows.
What it isn't
- Not a medical device and not a source of clinical or diagnostic advice.
- Not a wet-lab substitute — designs still need real validation at the bench.
- Not a data-harvesting cloud — nothing leaves your computer unless you fetch a public record.
- Not locked-in — export standard sequence and GenBank/GFF3 formats any time.
See it run on real data
A real walkthrough of the Nucleora interface — genuine ViennaRNA folding, genuine codon optimization, genuine manufacturability scoring. No mockups.
Watch the demo