Computer-aided gene design

Protein Eng. 1992 Dec;5(8):821-5. doi: 10.1093/protein/5.8.821.


A computer program, which runs on MS-DOS personal computers, 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 restriction sites can be accommodated. The nucleic acid sequence is then 'refined' according to a specific codon usage to remove any degeneration. Unique restriction sites, if potentially present, can be 'forced' into the degenerated nucleic acid sequence by using 'priority codes' assigned to different restriction sequences.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Codon
  • Computer-Aided Design*
  • Computers
  • Deoxyribonucleases, Type II Site-Specific / metabolism
  • Genes, Synthetic*
  • Molecular Sequence Data
  • Protein Engineering / methods*
  • Software*
  • Substrate Specificity


  • Codon
  • Deoxyribonucleases, Type II Site-Specific