From codon optimization to IVT simulation, Nucleora brings a full molecular biology workbench to your desktop — no cloud uploads, no subscriptions.
Re-code proteins for expression in any host organism — with real codon-usage data, not guesswork.
Choose from most-frequent, usage-weighted, CAI-guided, tAI-guided, or MFE-aware strategies.
Real RefSeq-derived codon tables for humans, cattle, elephants, primates, livestock, and more.
Documented clade-based proxies for species with limited genomic data — never silent about data quality.
Avoid restriction sites, deplete CpG/uridine, remove poly(A) signals — all as guarded synonymous rewrites.
See CAI, tAI, GC%, and uridine content change in real time as you optimize.
Balance competing objectives (CAI vs. MFE vs. uridine) with adjustable weights.
Assemble therapeutic-style mRNA constructs with provenance-cited parts.
Step-by-step workflow: antigen → optimization → full construct with UTRs, Kozak, signal peptide, poly(A).
m1Ψ, 5moU, and pseudouridine support with correct MW/extinction calculations.
Check CleanCap AG/AU, ARCA, and enzymatic capping requirements against your 5′ sequence.
Curated secretion leaders for MHC I, MHC II, and DC targeting applications.
Every element cites its source — know where each UTR, Kozak, and poly(A) comes from.
ORF integrity, frame checking, internal stop detection, and Kozak context grading.
ViennaRNA-powered structure prediction with immunogenicity risk analysis.
Minimum free energy, ensemble energy, centroid structure, and base-pairing probabilities.
ΔG calculations in cap-proximal and start-codon regions to predict translation efficiency.
Identify double-stranded regions that may trigger innate immune sensors.
Arc diagrams and interactive Forna-style 2D structure viewers.
Simulate in-vitro transcription runs before you reach the bench.
Scans for T7 promoter, +1 initiation, termination risks, homopolymers, and cryptic signals.
Model-based yield predictions based on scale, polymerase, and transcript properties.
T7 elongation rate and time-to-yield curves at different temperatures.
A–D graded report with severity-ranked issues and suggested fixes.
Itemized reagent list with quantities and indicative costs for your reaction scale.
Encapsulation predictions, N/P ratio suggestions, and four-lipid formulation notes.
Restriction mapping, assembly design, and primer3-powered primer generation.
Full REBASE database with unique-cutter identification, virtual digests, and fragment prediction.
Overlap calculation, primer design with correct overhangs, and homology checking.
Type IIS enzyme support, overhang design, and domestication primer generation.
PCR, sequencing, cloning, and IVT-template primers with Tm/dimer/hairpin analysis.
Circular and linear maps with feature annotations, restriction sites, and ORF indicators.
Find binding sites, predict amplicons, and check for off-target mispriming.
Sequence analysis, protein properties, and virtual bench assays.
Six-frame translation, ORF detection with configurable start codons and length filters.
Pairwise and multiple alignment with identity/gap visualization.
MW, pI, extinction coefficient, GRAVY, amino acid composition calculators.
Agarose gel simulation for restriction digests and PCR products with ladder calibration.
Import/export FASTA, GenBank, GFF3, EMBL — SnapGene-compatible annotations.
Antigenicity prediction, hydrophilicity plots, and surface-exposure scoring.
Connect to NCBI, UniProt, Ensembl, and PDB — with results cached locally.
Search by gene name, protein name, accession, or keyword across multiple databases.
Auto-detect ID types and fetch from the correct database automatically.
Extract signal peptides, domains, PTMs, and active sites as normalized features.
Search results are cached for offline access — fetch once, use anywhere.
Species-specific design for zoo animals, livestock, and endangered species.
Real data for elephants, primates, big cats, bears — not human-derived approximations.
Documented fallbacks for okapi, bongo, pangolin — with explicit "low data" warnings.
Weight-based dose estimates using published scaling factors.
Cattle, pigs, sheep, goats, chickens, horses — standard veterinary targets.
Watch a real walkthrough of the interface — genuine ViennaRNA folding, genuine codon optimization, genuine manufacturability scoring.