Efficient Codon Optimization with Motif Engineering

  • Anne Condon
  • Chris Thachuk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7056)


It is now common to add protein coding genes into cloning vectors for expression within non-native host organisms. Codon optimization supports translational efficiency of the desired protein product, by exchanging codons which are rarely found in the host organism with more frequently observed codons. Motif engineering, such as removal of restriction enzyme recognition sites or addition of immuno-stimulatory elements, is also often necessary. We present an algorithm for optimizing codon bias of a gene with respect to a well motivated measure of bias, while simultaneously performing motif engineering. The measure is the previously studied codon adaptation index, which favors the use, in the gene to be optimized, of the most abundant codons found in the host genome. We demonstrate the efficiency and effectiveness of our algorithm on the GENCODE dataset and provide a guarantee that the solution found is always optimal.


Codon Usage Codon Bias Codon Optimization Nucleic Acid Research Codon Adaption Index 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Anne Condon
    • 1
  • Chris Thachuk
    • 1
  1. 1.Department of Computer ScienceUniversity of British ColumbiaVancouverCanada

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