How it works — Nucleora

Find your antigen

Free-text search public databases: type something like "elephant endotheliotropic herpesvirus glycoprotein B" and pick a hit; it becomes your antigen in one click. No time for a live lookup? Paste a sequence directly, look up an Ensembl gene by symbol, or upload a FASTA/GenBank file. Every path is processed locally once the sequence is in hand.

Design the mRNA

Pick a target species and Nucleora tells you upfront whether the codon table is real (tallied from NCBI RefSeq coding sequences) or a documented proxy. Choose an optimization strategy (CAI-guided, max-usage, or usage-weighted), then layer on optional CpG depletion, uridine depletion, and restriction-site avoidance. Nucleora then assembles a full IVT-ready construct: T7 promoter, 5′UTR, Kozak, optional signal peptide, your codon-optimized

Review & export

See the Construct Health Score, the full quality scorecard (CAI, GC%, CpG, uridine fraction, start-codon accessibility), and a parts-and-provenance breakdown with citations for every element. Run the IVT simulation for a graded manufacturability report, price it out in Manufacture & order, then export GenBank, GFF3, FASTA, or a spec-sheet PDF.

Step 3 review and export screen showing the construct health score

Under the hood

A reusable engine, not a black box

The design engine has no web dependency and is importable on its own. Every number in the UI comes from the same code path a script would call directly.

sequence.py & codon.py

Translation, transcription, reverse-complement, ORFs, GC/Tm/MW, and codon optimization with CAI and CpG/uridine/GC constraints.

mrna.py & structure.py

Construct assembly from building blocks, plus ViennaRNA folding and the quality scorecard.

ivt.py & manufacture.py

IVT manufacturing-run simulation and manufacturability report, plus the quantitative yield/kinetics/order-form model.

restriction.py

Full restriction analysis over BioPython's REBASE set: 1,000+ enzymes.

databases.py & annotate.py

Ensembl / NCBI / UniProt clients, auto-annotation, and FASTA/GenBank import.

primers.py & cloning.py

Primer design and restriction/Gibson/Golden Gate assembly simulation.

from engine import mrna, structure
c = mrna.assemble("MEEPQSDPSV...", "human",
                  signal_peptide="human IgE leader (METDTLLLWVLLLWVPGSTG)",
                  cterm_tag="MHC-I trafficking (MITD, DC vaccines)",
                  opt_opts={"avoid_cpg": True})
print(c["length_mrna"], c["qc"]["cai"])
print(structure.qc_report(c)["score"])

One double-click, then it's yours

Quick start

macOS / Linux: double-click Start Nucleora.command. Windows: double-click Start Nucleora.bat. On first launch it creates a local Python environment, installs dependencies once, then opens the app in your browser. Later launches are instant.

Requirements

Python 3 (3.11 or 3.12 recommended). If macOS blocks the launcher as being from an unidentified developer, right-click → Open → Open, once. Or run it from Terminal withbash "Start Nucleora.command".

Three guided steps. A full lab platform if you want it.