Patent ID: 8812247
Filing Date: 2014-08-19
Classification: C12N

Abstract:
1. A computerized method of optimizing a nucleotide coding sequence coding for a predetermined amino acid sequence for expression in a predetermined host cell, the method comprising: (a) generating, using a suitably programmed computer, at least one coding sequence that codes for the predetermined amino acid sequence; (b) generating, using the suitably programmed computer, at least one newly generated coding sequence from at least one coding sequence by replacing in at least one coding sequence at least one codon by a synonymous codon; (c) determining, using the suitably programmed computer, a fitness value of said at least one coding sequence and a fitness value of said at least one newly generated coding sequence while using a fitness function that determines at least one of single codon fitness and codon pair fitness for the predetermined host cell; (d) choosing, using the suitably programmed computer, at least one selected coding sequence amongst said at least one coding sequence and said at least one newly generated coding sequence in accordance with a predetermined selection criterion such that the higher is said fitness value, the higher is a chance of being chosen; (e) repeating (b) through (d), using the suitably programmed computer, while treating said at least one selected coding sequence as at least one coding sequence in (b) through (d) until a predetermined iteration stop criterion is fulfilled, wherein g symbolizes a coding sequence, |g| its length, g(k) its k-th codon, r c target (c(k)) is a desired ratio of codon c(k) and r c g (c(k)) an actual ratio in the nucleotide coding sequence g.