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Codon Optimization Using a Recurrent Neural Network

J Comput Biol. 2022-06; 
Dennis R Goulet, Yongqi Yan, Palak Agrawal, Andrew B Waight, Amanda Nga-Sze Mak, Yi Zhu
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Gene Synthesis … The GenScript algorithm, for example, considers more than 200 known factors influencing … GeneArt and GenScript sequences were also low in thymine (19%–20%), but they showed … Get A Quote

摘要

Codon optimization of a DNA sequence can significantly increase efficiency of protein expression, reducing the cost to manufacture biologic pharmaceuticals. Although directed methods based on such factors as codon usage bias and GC nucleotide content are often used to optimize protein expression, undirected optimization using machine learning could further improve the process by capitalizing on undiscovered patterns that exist within real DNA sequences. To explore this hypothesis, Chinese hamster DNA sequences were used to train a recurrent neural network (RNN) model of codon optimization. The model was used to generate optimized DNA sequence based on an input amino acid sequence for the example receptor progra... More

關鍵詞

bioinformatics, codon optimization, machine learning, molecular biology, protein expression, sequence analysis
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