Codon Usage Preferences
Solving the riddle of codon usage preferences: a test for translational selection
... Since genome size and genomic tRNA number are highly correlated (R = 0.85), it seems logical to think that both factors co-evolve in a concerted way. The evolution of genome size has largely been related to the evolution ...
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Codon Usage in Hemoglobin Coding Genes
... in codon usage preferences in different organisms, meanwhile, codon usage preference not only plays an important regulatory role map at the level of gene expression, but also helps to ...
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Genome wide analysis of codon usage bias in Bovine Coronavirus
... from codon preferences [24], the expected CAI (e-CAI) values were calculated for BCoV complete genome ORFs sequences in relation to ...taurus codon usage reference ...with codon ...
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Codon usage bias and base composition of nuclear genes in Drosophila.
... Under the assumption that the rates and patterns of mutation in introns are the same as those of synonymous sites in the coding regions, we conclude that the variation in[r] ...
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Genomic adaptation of the ISA virus to Salmo salar codon usage
... host codon use”, and therefore also supports the notion that ISAV is an emerging pathogen, it being the least adapted viral Salmo salar pathogen and Orthomyxovi- rus to host codon usage and thus ...
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CAIcal: A combined set of tools to assess codon usage adaptation
... the codon preferences or whether they are merely artefacts that arise from internal biases in the G+C composition and/or amino acid composition of the query ...
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Codon bias of influenza a viruses and their hosts
... utilized codon volatility, where the volatility of a codon is the probability that a random point mutation will result in a nonsynonymous codon (a codon that does not encode the same amino ...
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Patterns and influencing factor of synonymous codon usage in porcine circovirus
... and codon preference, this result shows that nucleotide constraints have a major impact on its synonymous codon ...indicate codon usage patterns of PCV of various genotypes, various ...
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The selection-mutation-drift theory of synonymous codon usage.
... It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, wi[r] ...
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How Codon Usage Bias Affects Our Ability to Recover the Tree of Life
... Cognate, near-cognate, and non-cognate tRNA may attempt to bind to an mRNA codon. If relatively few cognate tRNA are available, translation will slow because other tRNA attempt to bind to the same codon. ...
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Analysis of codon usage and nucleotide composition bias in polioviruses
... Principal component analysis was carried out to identify the codon usage bias among ORFs. From which we could detect one major trend in the Axis 1 which accounted for 20.815% of the total variation, and ...
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P-value based visualization of codon usage data
... amino acids. Using the two complementary kinds of information exclusively, both methods provide com- pletely different approaches to codon usage analysis [22]. For the evaluation of the MDS-based ...
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Codon usage optimization in pluripotent embryonic stem cells
... Ribosome-protected RNA was isolated as described before [61, 74]. Briefly, at the indicated time points, H9 cells (4 replicates) were washed with PBS and lysed in 20 mM Tris-Cl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM ...
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Maximizing Transcription Efficiency Causes Codon Usage Bias
... It is much more difficult to distinguish THCU from the mutation hypothesis regarding the differences in codon usage among mammalian species of different metabolic rate[r] ...
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The omp2 Gene of HPS type Bacteria Cloning and Sequence Analysis Isolates from Sichuan Province
... of codon usage has certain dif- ferences; after CUSPS analysis, we found the gene sequence encoding the same amino acid with varying degrees of differ- ence in codon usage frequency, such as ...
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Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations
... Calculating F is a novel tool for addressing codon usage bias in genes and genomes. Here we applied this approach for comparing the whole genomes among species. F can be applied to study GC content shift ...
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Analysis of yeast codon usage patterns using the movable ORF collection
... the codon composition in the early portion of the transcript can dramatically affect protein expression levels [12, ...between codon usage and its expression ...start codon, exerting an ...
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Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias
... employing codon deoptimization or codon pair deoptimization (24–26), no significant overall reduction of pro- teins was found in our study ...different codon deoptimization strategies and virus ...
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Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes
... in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga ...
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Estimating translational selection in Eukaryotic Genomes
... particular codon preferences (Grantham et ...of codon usage in a given genome is given by a balance be- tween mutational bias, random genetic drift, and the action of natural selection (Sharp ...
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