Gene synthesis allows for instant access to any gene sequences imaginable, natural or not. Designing non-natural genetic sequences requires a ‘genetic CAD' software where functional elements can be treated as abstractions as well as physical entities. Manipulations of the sequences should be intuitive, flexible and feature-rich. The DNA2.0 software Gene Designer (freely available) uniquely addresses design issues for synthetic genetic constructs. Codon optimization enables the complete redesign of a DNA sequence while retaining the exact amino acid sequence required so that protein expression levels are maximized. The codon optimization algorithm developed by DNA2.0 is empirically tested by systematic analysis and thoroughly validated in several different hosts to ensure maximal translational control. The resulting algorithm reveals several unexpected variables controlling protein expression in heterologous hosts. Protein engineering using synthetic genes allows for complete control of the probed sequence space. Every defined point in the megadimensional sequence space can be independently investigated and systematically quantitated. The predefined gene variants (50-500) encoding systematically varied substitutions are tested in the real commercial high quality low throughput assay (no HTP assay) and the functional output of each sample is used to deconvolute the contribution of each substitution. Tools like these allow for fast, efficient, precise and consistent biocatalyst engineering.