FactorForge: constraint-aware CDS design and pre-synthesis sequence review for plant workflows

FactorForge is an open-source, constraint-aware coding sequence (CDS) design and pre-synthesis sequence review tool for plant molecular expression workflows, with primary support for Nicotiana benthamiana and experimental Tobacco BY-2 host context. It scores and ranks synonymous CDS candidates using a dynamic programming feasibility engine, reporting Codon Adaptation Index (CAI), GC content, PolyA motifs, rare-codon patterns, and Type IIS restriction-site conflicts with provenance tracking. Outputs are intended for in-silico review and require independent experimental validation; they do not guarantee expression, yield, synthesis acceptance, folding, glycosylation, regulatory approval, or downstream biological performance.