Everything a design studio needs, and the depth of a full lab platform underneath

Nucleora opens on a guided three-step vaccine workflow. Behind it sits a full sequence-editing, cloning, CRISPR, manufacturing, and compliance platform: 350+ individual tools, organized into nine workspaces.

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Sequence Workspace
  • Feature editor & auto-annotate
  • Circular / linear map (seqviz)
  • Domain scan (Pfam/InterPro)
  • Codon usage heatmap
  • Chromatogram viewer
47
Design Studio
  • mRNA designer & cloning
  • Codon tester (cross-tool verification)
  • Golden Gate matrix
  • Poly(A) & cap configuration
  • RNA structure & parts registry
44
Vaccine & Therapeutic Studio
  • One-click animal vaccine
  • GMP / CMC batch records
  • IVT scale-up cost model
  • Cold-chain & delivery planning
  • Lot comparability
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CRISPR & Genome Engineering
  • sgRNA design & on-target scoring
  • Paired nickase & base editing
  • Off-target scan
  • Editing templates
  • Screening library design
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Analysis & QC
  • Virtual gel & in-silico PCR
  • Pairwise / multiple alignment
  • Sanger & NGS QC
  • Peptide properties
  • Batch / plate QC
38
Virtual Lab & Simulation
  • 44 interactive in-silico experiments
  • Expression timecourse
  • Stability stress testing
  • Immunogenicity profile
  • Species physiology profile
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Databases & Knowledge Hub
  • Unified search — NCBI, UniProt, Ensembl
  • PDB structures & AlphaFold/InterPro
  • ChEMBL, KEGG & STRING, Rfam
  • Deep dossier & antigen evidence
  • ID mapping & homology search
18
Compliance & Regulatory
  • Regulatory pathway planner
  • IBC protocol builder
  • 21 CFR 11 e-signature & audit trail
  • CMC document assembler
  • Live regulatory feed
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Collaboration, Data & Platform
  • Version control & diff viewer
  • Sharing & access, comments
  • LIMS / ELN integration
  • Synthesis order routing
  • Classroom / digest mode
The flagship workflow

Codon optimization that knows the difference between real data and a best guess

Type an animal: elephant, tiger, panda, any species. Nucleora tells you plainly whether it has real codon usage tallied from RefSeq coding sequences, or whether it's optimizing against a documented, clade-anchored proxy. Nothing is silently approximated.

Target species picker with real vs proxy codon data badges
Quality, not just a sequence

A Construct Health Score you can actually read

Every finished construct gets a weighted score (CAI, GC%, CpG, uridine fraction, start-codon accessibility, translation, and the presence of T7/Kozak/poly(A)), a full parts-and-provenance breakdown with citations, and one-click GenBank, GFF3, FASTA, and spec-sheet PDF export.

Construct Health Score and quality scorecard for a designed mRNA
Simulate and check IVT panel with manufacturability grade

Simulate the manufacturing run before it costs you anything

The “Simulate & check” panel walks your template through linearization, T7 transcription, capping, and poly(A) tailing, then produces a graded (A–D / Fail) manufacturability report. It flags missing promoters, ORF/frame errors, homopolymer runs, cryptic polyadenylation signals, dsRNA/immunostimulation risk, and more, each with a plain-language fix.

From design to order form

Manufacture & order — a transparent, itemized estimate

Enter a reaction spec (volume, NTP concentration, template mass, T7 units and enzyme-lot activity, temperature, time, cap method, modified-U, µg/dose) and Nucleora computes yield as the smallest of three physical

Manufacture and order panel with reaction spec form

See these features in motion

A real, unscripted walkthrough of the actual engine. No mockups, no staged data.

Watch the demo