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Codon bias from minimization of codon–anticodon interaction
Biosystems, 2016Inequalities between codon usage probabilities for quartets of codons are derived using a minimum principle for codon-anticodon interaction and a probability sum rule in the framework of the Crystal Basis Model of the genetic code. Performing this study separately for the Early and for the Eukaryotic Genetic Code, we observe a consistency in the ...
Sciarrino, Antonino, Sorba, Paul
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Codon Usage in Trypanosomatids: The Bias of Expression
Trends in Parasitology, 2018Translation and RNA decay, two processes in which all mRNAs are engaged, are intimately related processes. Two new studies demonstrate that, in trypanosomatids, codon usage largely shapes mRNA abundance in a translation-dependent manner. The findings indicate that mRNA decay control by codon choice is an ancient and conserved mechanism.
Esteban D, Erben, Christine, Clayton
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Codon usage bias in herpesvirus
Archives of Virology, 2010In this study, I present a comprehensive analysis of codon usage bias in 43 herpesviruses for which the whole genome has been sequenced. The values of the effective number of codons revealed that the majority of the herpesviruses did not have high codon bias, with the exceptions of only simplexviruses and some varicelloviruses.
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Codon bias and heterologous protein expression
Trends in Biotechnology, 2004The expression of functional proteins in heterologous hosts is a cornerstone of modern biotechnology. Unfortunately, proteins are often difficult to express outside their original context. They might contain codons that are rarely used in the desired host, come from organisms that use non-canonical code or contain expression-limiting regulatory ...
Claes, Gustafsson +2 more
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Codon usage bias of Catharanthus roseus
China Journal of Chinese Materia Medica, 2016This study aimed to provide guidance for the heterogenous gene expression, gene prediction and species evolution by analyzing codon usage bias of Catharanthus roseus.The codon composition and usage bias of 30 437 high-confidence coding sequences from C.roseus were analyzed and the proportion of rare codons of Escherichia coli and Saccharomyces ...
Ying, Li +4 more
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Codon Usage Bias and tRNA Abundance in Drosophila
Journal of Molecular Evolution, 1997Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development. We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the ...
E N, Moriyama, J R, Powell
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PICDI, a simple program for codon bias calculation
Molecular Biotechnology, 1996PICDI is a very simple program designed to calculate the Intrinsic Codon Deviation Index (ICDI). The program is available in Macintosh as well a PC format. Requirements for correct input of the sequences have been kept to a minimum and the analysis of sequences up to 2000 codons is very quick.
E, Rodríguez-Belmonte +5 more
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Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA)
2017One 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 usage bias in metagenomes
2008Codon usage (CU) bias is an effect predominant in prokaryotes whereby synonymous codons are used with different frequencies between different species and even between genes within a single genome. This effect is related to tRNA abundance and can be used to predict expressivity of proteins by comparing their CU with that of a reference set of ...
Vlahoviček, Kristian, Lucić, Vedran
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