Patent ID: 8175813
Filing Date: 2012-05-08
Classification: G16B

Abstract:
1. A method of optimizing a nucleotide sequence for expression in a target organism comprising: a) providing a nucleotide sequence of interest; b) providing a target database of nucleotide sequences, wherein the database is specific to a genus of the target organism; c) compiling a list of all possible N-length nucleotide sequences (NLS) for a given length of N, wherein N is less than the length of the shortest nucleotide sequence in the database, and wherein N is constant for each NLS; d) obtaining an observed frequency value for each NLS by counting the number of times each NLS is represented in the database and dividing by the total number of NLSs observed in the database; e) calculating the probability score for each NLS identified in step (c) with respect to the database provided in step (b) to generate an NLS Statistics Table, wherein the probability score represents the observed frequency of each NLS relative to its expected frequency of occurrence within the target database; f) identifying for one or more N-length region(s) (NLRs) of the nucleotide sequence of interest a corresponding set of NLSs that does not alter the amino acid sequence encoded by the nucleotide sequence of interest, wherein an NLS that does not alter the amino acid sequence encoded by the nucleotide sequence of interest is considered a silent NLS (SNLS), and wherein the length of N in the NLR is equal to the length of N in the NLS; g) calculating a delta score for each SNLS, wherein the delta score represents the difference between the probability score of the NLR of the nucleotide sequence of interest and each corresponding SNLS; h) substituting one or more NLRs in the nucleotide sequence of interest with the corresponding SNLS having the largest delta score to generate an optimized sequence; and i) chemically synthesizing a nucleic acid molecule consisting of the optimized nucleotide sequence for expression in the target organism.