How It Works

FactorForge runs a deterministic constraint-based pipeline in four stages:

Protein sequence (FASTA or plain text)
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1. Reverse Translation
   Selects synonymous codons to maximize CAI
   against the selected host codon usage table
   (N. benthamiana by default; --host by2 for Tobacco BY-2)
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2. Rule Scan
   Detects PolyA signals, homopolymers,
   CpG/TpA dinucleotide hotspots,
   repeat sequences, rare codon runs,
   forbidden restriction sites
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3. Domestication
   Removes Golden Gate / MoClo-incompatible
   BsaI / BsmBI recognition sites via silent edits
   Optional custom restriction sites removed
   CpG/TpA reduction with CAI-budgeted balanced mode
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4. Output
   Optimized CDS — FASTA or GenBank
   with full metrics and scan report

Engines

Engine	Flag	Description
dp	--engine dp	DP feasibility engine (default) — constraint-based, deterministic
profile	--engine profile	Rule/profile optimizer — profile-driven CAI and constraint handling

Design Objectives

Objective	Description
feasibility_best	Best achievable CAI/GC under synonymous constraints (default)
gc_target	GC-focused rule-based output
high_cai	CAI-focused rule-based output