Patent ID: 8224578

Claim:
A computerized method for optimizing a nucleotide sequence for the expression of a protein on the basis of the amino acid sequence of the protein, which comprises the following steps: generating, using a suitably programmed computer, a first test sequence of n codons which correspond to n consecutive amino acids in the protein sequence, where n is a natural number and is less than N, the number of amino acids in the protein sequence, specifying, using the suitably programmed computer, m optimization positions in the test sequence which correspond to the position of m codons at which the occupation by a codon, relative to the test sequence, is to be optimized, where m≦n and m<N, generating, using the suitably programmed computer, one or more further test sequences from the first test sequence by replacing at one or more of the m optimization positions a codon of the first test sequence by another codon which expresses the same amino acid, assessing, using the suitably programmed computer, each of the test sequences with a quality function and ascertaining the test sequence which is optimal in relation to the quality function, specifying, using the suitably programmed computer, p codons of the optimal test sequence which are located at one of the m optimization positions, as result codons which form the codons of the optimized nucleotide sequence at the positions which corresponds to the position of said p codons in the test sequence, where p is a natural number and p≦m, iterating the preceding steps, where in each iteration step the test sequence comprises the appropriate result codon at the positions which correspond to positions of specified result codons in the optimized nucleotide sequence, and the optimization positions are different from positions of result codons.