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FactorForge

Open-source constraint-based CDS design engine for plant expression workflows, with initial focus on Nicotiana benthamiana and Tobacco BY-2.

License PyPI CI codecov DOI

FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports N. benthamiana (agroinfiltration) and Tobacco BY-2 (--host by2, bioreactor/cGMP).

Quick Start

pip install factorforge-cds
factorforge optimize my_protein.fasta -o output.fasta

Or use the web app — no installation required.

Access Options

Method Description
Web App No installation, demo & light use
CLI / Python Local use, batch processing, data privacy
Docker Full web interface locally, no data leaves your machine

Performance

Benchmarked on N. benthamiana SGN CDS (v3.1.4, balanced profile, N=3,876 sequences):

Metric Value Target
CAI (mean) 0.76 ≥ 0.75
GC% (mean) 59.77% 55–65%
AA identity 100% 100%
Validator pass rate 100% 100%

Supported Hosts

Host Status
Nicotiana benthamiana ✅ Supported (--host nbenthamiana, default)
Tobacco BY-2 (N. tabacum) ⚠️ Experimental (--host by2)
Wolffia globosa 🔶 Codon table available, coming soon
Other plant hosts 📋 Planned

Validation Status

FactorForge predictions are in-silico only and have not been experimentally validated in wet-lab conditions. See Validation for details.