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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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Condon Optimization: Codon Optimization of Therapeutic Proteins: Suggested Criteria for Increased Efficacy and Safety
Proteins are amongst the most useful and effective molecules for a range of applications, including industrial enzymes and therapeutics. Some...
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Application of Codon Optimization and Recombinant Expression of Beta-Glucanases
Beta-glucanases are industrially important glucan hydrolyzing enzymes. Beta-glucanase produced from Streptomyces sp. is more efficient and highly...
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Relative synonymous codon usage and codon pair analysis of depression associated genes
Depression negatively impacts mood, behavior, and mental and physical health. It is the third leading cause of suicides worldwide and leads to...
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Intensification Process Applied to Codon Selection in Grammatical Evolution
Grammar Evolution (GE) represents a variant of Genetic Programming that has gained substantial popularity in recent years within the field of...
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Codon optimization of a gene encoding DNA polymerase from Pyrococcus furiosus and its expression in Escherichia coli
BackgroundDNA polymerase is an essential component in PCR assay for DNA synthesis. Improving DNA polymerase with characteristics indispensable for a...
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Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
BackgroundCodon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare...
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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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An exploratory in silico comparison of open-source codon harmonization tools
BackgroundNot changing the native constitution of genes prior to their expression by a heterologous host can affect the amount of proteins...
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Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson’s Disease
Codon usage bias (CUB) is the phenomenon of non-uniform usage of synonymous codons in which some codons are more used than others and it helps in...
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Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough
Stop codon readthrough events give rise to longer proteins, which may alter the protein’s function, thereby generating short-lasting phenotypic...
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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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Analysis of codon usage bias of thioredoxin in apicomplexan protozoa
BackgroundApicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as...
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Codon usage and evolutionary dynamics of genetic diversity of novel imported porcine reproductive and respiratory syndrome virus in China
Porcine reproductive and respiratory syndrome (PRRS) is a problem that has significant economic impact on the global pig industry. In recent years,...
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Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon
Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is...
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The evolutionary characterization of Gamasida based on mitochondrial genes codon usage pattern
Mites belonging to the suborder Gamasida are species-rich and habitat-diverse, with a worldwide distribution. To adapt to the environment and obtain...
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Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use...
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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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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...
