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ICOR: improving codon optimization with recurrent neural networks
BackgroundIn protein sequences—as there are 61 sense codons but only 20 standard amino acids—most amino acids are encoded by more than one codon....
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Using protein-per-mRNA differences among human tissues in codon optimization
BackgroundCodon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized...
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Tailoring Codon Usage to the Underlying Biology for Protein Expression Optimization
For heterologous gene expression, codon optimization is required to enhance the quality and quantity of the protein product. Recently, we introduced...
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Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome...
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Assessing optimal: inequalities in codon optimization algorithms
BackgroundCustom genes have become a common resource in recombinant biology over the last 20 years due to the plummeting cost of DNA synthesis. These...
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Effects of codon optimization, N-terminal truncation and gene dose on the heterologous expression of berberine bridge enzyme
Morphine, sanguinarine and chelerythrine are benzylisoquinoline alkaloids (BIAs), and these compounds possess strong biological activities. ( S )-scoule...
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SARS-CoV-2 continuously optimizes its codon usage to adapt to human lung environment
Viruses need to utilize the resources from host cells to reproduce themselves. RNA translation rate, which is largely determined by codon usage, is...
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Codon usage bias
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals....
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Compositional Dynamics and Codon Usage Pattern of Myogenin (MyoG) Gene across Different Mammalian Species
AbstractMyoG enin ( MyoG ) is one of the key regulatory factors for controlling the generation of skeletal muscle. Codon usage bias (CUB) as a unique...
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An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea
BackgroundThe chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant...
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Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species
Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of...
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Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina
BackgroundHemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and...
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Codon optimization of the synthetic 3-ketosphinganine reductase (3KSR) protein for enhancing sphingolipid biosynthetic enzyme expression
BackgroundSphinganine is a key precursor for the synthesis of ceramide during sphingolipid biosynthesis in eukaryotes. In the sphinganine...
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Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV’s oncogenic role
Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins....
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Influence of codon optimization, promoter, and strain selection on the heterologous production of a β-fructofuranosidase from Aspergillus fijiensis ATCC 20611 in Pichia pastoris
Fructooligosaccharides (FOS) are compounds possessing various health properties and are added to functional foods as prebiotics. The commercial...
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Codon usage patterns across seven Rosales species
BackgroundCodon usage bias (CUB) analysis is an effective method for studying specificity, evolutionary relationships, and mRNA translation and...
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Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino...
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Optimization of Enzymes
This chapter describes the strategies for the optimization of enzymes for industrial applications using protein engineering methods. Firstly, the two...
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Adaption of tobacco rattle virus to its solanaceous hosts is related to the codon usage bias of the hosts and that of the viral 16 K gene
Tobacco rattle virus (TRV) is a member of the genus Tobravirus , family Virgaviridae , that infects many different plants from 50 families. TRV-based...
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Development of an Agrobacterium-delivered codon-optimized CRISPR/Cas9 system for chickpea genome editing
Chickpea is considered recalcitrant to in vitro tissue culture amongst all edible legumes. The clustered, regularly interspaced short palindromic...
