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 favor 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 (9 advisory scanners, run by default)
   Detects PolyA signals, AU-rich elements,
   AT-rich runs, homopolymers, tandem repeats,
   local GC extremes, splice-like motifs,
   CpG/TpA dinucleotide hotspots, rare codon runs
   (advisory findings only — never gating)
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3. Domestication
   Removes Golden Gate / MoClo-incompatible
   BsaI / BsmBI recognition sites via silent edits
   (halts if unresolvable)
   Optional custom restriction sites removed
   CpG/TpA reduction with CAI-budgeted balanced mode
   MoClo overhang validity/collision check available
   when building a construct (opt-in, non-gating)
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4. Output
   Designed 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

The DP engine (--engine dp) supports one --objective:

Objective	Description
feasibility_best	Best achievable CAI/GC under synonymous constraints (default)

The profile engine (--engine profile) supports these --profile values (not DP --objective values — passing gc_target or high_cai to --objective always fails, since the DP engine only implements feasibility_best; see Optimization Profiles):

Profile	Description
gc_target	GC-focused rule-based output
high_cai	CAI-focused rule-based output