CodonGenie: optimised ambiguous codon design tools

PeerJ Computer Science

卷:3

Philip J. Day¹  Lucy Green²  Andrew Currin²  Rainer Breitling²  Neil Swainston²  Douglas B. Kell² 

[1] Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom;

[2] Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), University of Manchester, Manchester, United Kingdom;

关键词: Directed evolution;    Codon;    Protein engineering;    Industrial biotechnology;    Mutagenesis;    Enzyme engineering;   

DOI  :  10.7717/peerj-cs.120

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown