CodonGenie: optimised ambiguous codon design tools

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1 Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), University of Manchester, Manchester, United Kingdom
2 School of Chemistry, University of Manchester, Manchester, United Kingdom
3 Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
DOI
10.7287/peerj.preprints.2797v1
Published
Accepted
Subject Areas
Bioengineering, Bioinformatics, Biotechnology, Computational Biology, Synthetic Biology
Keywords
directed evolution, codon, protein engineering, industrial biotechnology, mutagenesis, enzyme engineering
Copyright
© 2017 Swainston et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Swainston N, Currin A, Green L, Breitling R, Day PJ, Kell DB. 2017. CodonGenie: optimised ambiguous codon design tools. PeerJ Preprints 5:e2797v1

Abstract

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. 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.

Author Comment

This is a submission to PeerJ Computer Science for review.