CodonGenie: Optimised ambiguous codon design tools

Neil Swainston, Andrew Currin, Lucy Green, Rainer Breitling, Philip J. Day, Douglas B. Kell

Research output: Contribution to journalArticlepeer-review


CodonGenie, freely available from, is a simple web application for designing ambiguous codons to support protein mutagenesis applica- tions. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence degeneracy when synthesised in a DNA library. In directed evolution studies, such codons are carefully selected to encode multiple amino acids. For example, the codon NTN, where the code N denotes a mixture of all four nucleotides, will encode a mixture of phenylalanine, leucine, isoleucine, methionine and valine. Given a user-defined target collection of amino acids matched to an intended host organism, CodonGenie designs and analyses all ambiguous codons that encode the required amino acids. The codons are ranked according to their efficiency in encoding the required amino acids while minimising the inclusion of additional amino acids and stop codons. Organism-specific codon usage is also considered.

Original languageEnglish
Article numbere120
JournalPeerJ Computer Science
Issue number7
Publication statusPublished - 10 Jul 2017


  • Codon
  • Directed evolution
  • Enzyme engineering
  • Industrial biotechnology
  • Mutagenesis
  • Protein engineering

Research Beacons, Institutes and Platforms

  • Manchester Institute of Biotechnology


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