Computer-aided Gene Design

A computer program, which runs on MS-DOS personal computer, is described that assists in the design of synthetic genes coding for proteins. The goal of the program is the design of a gene which (i) contains as many unique restriction sites as possible and (ii) uses a specific codon usage, The gene designed according to the criteria above is (i) suitable for modular mutagenesis experiments and (ii) optimized for expression. The program reverse translates protein sequences into degenerated DNA sequences, generates a map of potential restriction sites and locates sequence positions where unique restiction sites can be accomodated. The nucleic acid sequence is refined according to specific codon usage to remove any degeneration.