title: A Web Interface for Codon Compression.
abstract: Saturation mutagenesis is widely used in protein engineering and other experiments. A common practice is to utilize the single degenerate codon NNK. However, this approach suffers from amino acid bias and the presence of a stop codon and of the wild type amino acid. These extra features needlessly increase library size and consequently downstream screening load. Recently, we developed the DYNAMCC algorithms for codon compression that find the minimal set of degenerate codons, covering any defined set of amino acids, with no off-target codons and with redundancy control. Additionally, we experimentally demonstrated the advantages of this approach over the standard NNK method. While the code is freely available from our Web site, we have now made this method more accessible to a broader audience without any computational background by building a user-friendly web-based interface for those algorithms. The Web site can be accessed through: www.dynamcc.com .
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States.
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Halweg-Edwards
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States.
authors.forename: Gur
authors.initials: G
authors.lastname: Pines
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States.
authors.forename: James D
authors.initials: JD
authors.lastname: Winkler
authors.forename: Assaf
authors.initials: A
authors.lastname: Pines
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States.
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Gill
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000235:genetics; D003062:Codon / Q000235:genetics*; D015723:Gene Library; D005815:Genetic Code / Q000235:genetics*; D016296:Mutagenesis / Q000235:genetics; D015202:Protein Engineering / Q000379:methods
chemical_list: D000596:Amino Acids; D003062:Codon
keywords: codon compression; protein engineering; saturation mutagenesis; synthetic biology