A method for optimizing a nucleotide sequence for maximizing the expression of a protein in a predefined organism on the basis of the amino acid sequence of the protein, the method comprising the following steps which are carried out on a computer: a) generating 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 or equal to N, the number of amino acids in the protein sequence, b) specifying 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, c) generating 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, d) assessing each of the test sequences with a quality function and ascertaining the test sequence which is optimal with respect to the quality function, the quality function taking into account one or more of the following criteria: codon usage for a predefined organism, GC content, repetitive sequences, secondary structures, inverse complementary sequence repeats, and sequence motifs, e) specifying 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 correspond to the position of said p codons in the test sequence, where p is a natural number and p ≤ m, and iterating the preceding steps a) through e), wherein in each iteration step the test sequence contains 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. a) generating 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 or equal to N, the number of amino acids in the protein sequence, b) specifying 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, c) generating 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, d) assessing each of the test sequences with a quality function and ascertaining the test sequence which is optimal with respect to the quality function, the quality function taking into account one or more of the following criteria: codon usage for a predefined organism, GC content, repetitive sequences, secondary structures, inverse complementary sequence repeats, and sequence motifs, e) specifying 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 correspond to the position of said p codons in the test sequence, where p is a natural number and p ≤ m, and