Output Format
Each optimized sequence includes:
| Field | Description |
|---|---|
| Optimized CDS | Synonymous codon replacements only — AA identity 100% |
| CAI score | Codon adaptation index for the selected expression host |
| GC content | Global and first-region (first 90 nt) |
| Scan report | PolyA signals, CpG/TpA hotspots, homopolymers, rare codon runs, restriction sites |
| Domestication report | BsaI/BsmBI and custom restriction sites removed, edit count |
| Construct ID | Reproducible hash for tracking and reproducibility |
FASTA Output
GenBank Output
GenBank format includes all metadata as FEATURES annotations, suitable for direct import into sequence editing tools (Benchling, SnapGene, etc.).
Validator Contract
All outputs are guaranteed to pass the hard-fail validator:
| Check | Requirement |
|---|---|
| Amino acid identity | 100% |
| Internal stop codons | 0 |
| Invalid codons | 0 |
| Sequence length | Correct (input AA × 3) |
If any check fails, no output is produced.