Validation

Status

FactorForge is an in-silico only tool. It optimizes codon usage, GC content, and sequence constraints — but it cannot guarantee protein expression, yield, solubility, or folding in your specific system.

Warning

Wet-lab validation is always required before use in production workflows.

What FactorForge Checks

Check	Covered	Notes
Internal stop codons	✅	Hard fail
Amino acid identity	✅	Hard fail
GC% range	✅	Host-dependent; default N. benthamiana: 55–65%
Forbidden restriction sites	✅	BsaI, BsmBI, BpII (Golden Gate)
Invalid codons	✅	Hard fail
Rare codon runs	✅	Ribosome stalling risk detection
CpG/TpA dinucleotides	✅	CAI-budgeted reduction
Protein folding	❌	Requires wet-lab or AlphaFold
Actual expression level	❌	Requires wet-lab
Yield / solubility	❌	Requires wet-lab
Signal peptide behavior	❌	Requires wet-lab
Membrane protein topology	❌	Requires wet-lab

Contribute Wet-Lab Results

If you tested a FactorForge-optimized sequence in the lab, please share your result — positive or negative. Failed experiments are just as valuable.

→ Submit via Google Form (recommended)

Or open a GitHub Issue with the label wet-lab-result.

Please include:

• Host organism and protein
• FactorForge version and optimization profile
• Expression system and assay
• Result (qualitative or quantitative)
• Promoter, subcellular targeting, harvest timepoint (optional)
• Whether a native/unoptimized sequence was used as a control

Contributors will be credited in VALIDATION.md and future releases.