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Codons and Hypercycles

Origins of life and evolution of the biosphere, 1999
Several hypotheses on the origin of codon assignments imply that the present protein synthesizing machinery was already in place when the assignments were made. These are examined by computer modeling. The results do not suggest that assignments were optimized for resistance to reading and mutation errors, nor that the assignments are random.
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Tandem Stop Codons in Ciliates That Reassign Stop Codons

Journal of Molecular Evolution, 2009
Tandem stop codons are extra stop codons hypothesized to be present downstream of genes to act as a backup in case of read-through of the real stop codon. Although seemingly absent from Escherichia coli, recent studies have confirmed the presence of such codons in yeast.
Marie, Adachi, Andre R O, Cavalcanti
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Writing Scrapie's Coda, Codon by Codon?

Science, 2000
Over the past decade, geneticists have found that different variations, or polymorphisms, in the gene coding for PrP--a cellular protein that many scientists believe becomes infectious when it converts to an abnormal form called a prion--seem to confer varying degrees of susceptibility to scrapie.
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Codon optimizer: a freeware tool for codon optimization

Protein Expression and Purification, 2003
Selection plays a major role in the determination of codon usage in all organisms studied so far. In highly expressed genes, a narrow set of codons is used and these codons correspond to the more abundant tRNA species. This minimizes the risk of tRNA depletion during translation.
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Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA)

2017
One amino acid is added to a growing peptide by a ribosome through reading triple nucleotides, i.e., a codon, each time. Twenty species of amino acids are often coded by 61 codons, so one amino acid can be coded by more than one codon and the codons coding the same amino acid are called synonymous. Intriguingly, synonymous codons' usage is often uneven:
Zhenguo, Zhang, Gaurav, Sablok
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Codon

2008
Beata Gabrys   +97 more
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Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding

Annual Review of Biochemistry, 2021
Yi Liu, Qian Yang, Fangzhou Zhao
exaly  

Codon optimality, bias and usage in translation and mRNA decay

Nature Reviews Molecular Cell Biology, 2017
Jeff Coller
exaly  

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