Step 1 — Find your antigen
Query UniProt and NCBI Protein for the target sequence, e.g. elephant endotheliotropic herpesvirus glycoprotein B. Selecting a hit sets it as the antigen for the steps below; the accession and organism travel with it into the GenBank export. See Getting started for a worked example.
Other ways to get a sequence
Step 2 — Design the mRNA
Assembles 5′ UTR + signal peptide + codon-optimized ORF + C-terminal tag + 3′ UTR + poly(A), optimizing codon usage against the selected organism’s usage table. Every parameter below is explicit and editable; the values shown are the current ones, not hidden presets.
[REG] Regulations for this step →Multi-antigen design — encode 2+ antigens in one mRNA (polyvalent vaccine)
Add two or more antigens joined by a linker. Self-cleaving 2A elements release each antigen as a separate protein; flexible/rigid linkers keep them as one fusion. Per-antigen provenance is preserved on the map and in the GenBank export.
Multivalent co-encapsulation pool — mix 2+ SEPARATE mRNAs in one LNP at defined ratios
For a multivalent vaccine made of separate single-antigen mRNAs (not one fused ORF) mixed together before LNP formulation. Choose how the dose is split across components.
mRNA components (defaults are Moderna/BioNTech-style)
Parts bin — browse the UTR / leader library
A less-negative 5′ ΔG means less structure at the cap → easier ribosome scanning. Strong 5′ structure can raise stability but block initiation (see Structure tools).
Advanced sequence options
Recognition sites are removed on both strands (a non-palindromic enzyme like BsaI cuts even when its site is on the antisense strand). Enzyme names (BsaI, BbsI, SapI…) are resolved to their sequences automatically. Restriction-site removal never changes the encoded protein.
Some adjacent codon pairs are used far more/less than expected. Minimizing codon-pair bias is a published virus-attenuation strategy; maximizing it can raise expression. The host codon-pair reference is learned from RefSeq on first use.
Multi-objective explorer (CAI · tAI · 5′ structure)
Codon choice trades three goals: CAI (matches host codon usage), tAI (matches host tRNA supply), and 5′ MFE (an unstructured 5′ end loads ribosomes better). Set how much you care about each, then explore the Pareto-optimal designs — no design is better on all three at once.
Step 3 — Review & export
Construct sequence, per-metric QC table (CAI, GC%, MFE, cryptic sites, homopolymer runs) and the annotated feature map. Exports as FASTA, GenBank or plain sequence.
Synthesis order & LIMS
Turn a finished construct into a gene-synthesis order in each vendor's format, run manufacturability pre-checks, or push it to your LIMS.
[REG] Regulations for this step →Gene-synthesis order (Twist / IDT / GenScript)
LIMS bridge (Benchling / custom)
Vaccination Studio
Runs the full sequence in order: codon optimization, assembly, chemistry correction, dose scaling, LNP formulation, delivery-route physics, herd sizing, cold-chain and cost, then biosafety and environmental-release export. Each output carries its derivation label (physics-based, literature-value, trained-model or heuristic) and its source; open About & Methods for the full method registry.
[REG] Regulations for this step →Population & herd dosing (optional — for herd-immunity campaigns)
Virtual Lab Bench
In-silico counterparts of the standard validation experiments, run against the designed construct. Simulate the IVT reaction & RNA QC, predict the protein-expression timecourse, stress-test stability, and profile immunogenicity. Pick a species to scale the kinetics to that animal (mass and body-temperature as two separate axes) and open a cross-species physiology & allometry profile — metabolic rate, heart rate, blood volume, lifespan, each measured-where-known or an allometric prediction with its confidence, range and citation. Every result is computed from the construct’s own sequence, and each experiment emits a corresponding wet-lab protocol.
project_docs/docs/Research_Data.txt). The expression timecourse is a relative curve (not an absolute amount); the immunogenicity experiment reports a qualitative band with reasons and no numeric antibody titer — there is no honest quantitative titer model without wet-lab animals. Use the downloadable protocols to run the real experiments under your IBC/IACUC oversight. Not veterinary, clinical, or regulatory advice.Engagement Lab
Assembles a summary of this tool’s outputs for a chosen audience, ordering the selected points by how much evidentiary weight each carries. Every point is tagged by how much weight it can bear — physics-derived, published-method, library-delegated, calibrated-anchor, heuristic, or planning-grade — so a calibrated estimate never gets heard as a measured fact. The one preliminary set (LNP formulation, budget, shelf-life) is held in a separate hold-back drawer so it doesn't leak into a first message.
Talking points
Borrow one surprising-rigor point (audience-agnostic credibility anchor)
Assembled message
Hold back — real, but preliminary
Sequence editor
The active sequence as an editable feature map and as text. Edits recompute the map, translation and statistics on input.
Features
| Name | Type | Start | End | Strand | Color |
|---|
Cloning & assembly
Simulates junction sequences, checks overhang and site compatibility, and reports the predicted assembly product for the selected strategy.
[REG] Regulations for this step →PCR primers
IVT-template preset
Virtual agarose gel
Predicts fragment migration distances for a template, mRNA, digest products or PCR amplicons against a selected ladder, from fragment length and gel percentage.
RNA mode — TapeStation / denaturing simulator (IVT QC)
Sequencing QC — Sanger & NGS fidelity
Two orthogonal fidelity checks: confirm a clone with a Sanger .ab1 chromatogram, or measure synthesis error rate from deep-sequencing reads of the IVT product.
In-silico PCR
Find where a primer pair binds a template and predict the amplicon(s) — catches non-specific priming and wrong orientation before the bench.
Peptide property calculator
Molecular weight, isoelectric point, extinction coefficient (for A280 quantitation), net charge, and hydropathy of the expressed antigen.
Alignment
Compare two sequences (pairwise, global or local) or align many at once (multiple sequence alignment). Reports % identity and a match track.
Multiple sequence alignment
Align 3+ sequences at once (e.g. one antigen's orthologs across species) by the center-star method. Paste sequences in FASTA, or one per line.
History tree
Each transform (codon optimization, UTR addition, manual edit, assembly) is recorded as a node, branching where alternatives were explored. Selecting a node restores the editor to that exact sequence state.
Gene origins
Where every piece of the construct comes from — organism, database accession, and why it's here. The same source data annotates the GenBank export, so the origins travel with the file into any standard plasmid-map viewer.
Align to reference — sequencing QC
The reality check: paste your intended design (reference) and the sequencing result you got back, and Nucleora lists every difference — substitutions, insertions, deletions — with exact positions. Point out the ORF and it tells you whether a change is silent, missense, or a premature stop.
Calibration & verification
Nucleora runs a growing suite of automated self-checks against known bioinformatics calculation errors and edge cases — off-by-one indexing, circular origin crossings, modified-nucleotide mass, nearest-neighbor Tm, cap mismatches, folding temperature, GenBank round-trip, LNP/dose scaling, plasmid backbones, and more. Run them any time to verify the math and physical predictions are sound on this machine.
Engine self-test
Codon tester
Runs the coding sequence through several independent third-party codon-analysis packages and reports each tool’s metrics side by side, so agreement (or disagreement) with this app’s own figures is visible. Tools whose output has been checked against a reference case are listed first; the rest are marked unverified.
Cross-tool concordance report
Runs every installed tool on the same coding sequence and lays their metrics side by side. When independent implementations of the same index land on the same number, the result is reproducible — not a Nucleora artifact. This is the report to hand a skeptical lab.
Full validation report i
One report combining every independent check Nucleora runs on this coding sequence — not just CAI: protein-identity round-trip, GC-target fit, dinucleotide (CpG/UpA) bias, restriction-site cleanliness, mRNA secondary-structure delta vs. an unoptimized baseline, and (optionally) cross-tool CAI concordance — combined into one composite quality score with a full breakdown underneath.
Codon harmonization & rhythm i
Paste a native coding sequence (DNA) and re-code it for a new host by matching each codon's relative rank rather than maximizing usage — preserving the translational rhythm that aids folding (Angov 2008). Also reports codon-pair bias and rare-codon clusters.
Compliance Planner
Describe what your project actually does, and this planner maps it to the biosafety, biosecurity, and legal regulations that may apply — at each step of the Nucleora workflow. Every raised item says why it was raised (which project feature triggered it), who administers it, its legal basis, and links to the source. Export a per-project checklist to attach to your records.