[PDF] Top 20 Analysis of codon usage and nucleotide composition bias in polioviruses
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Analysis of codon usage and nucleotide composition bias in polioviruses
... differs greatly among organisms. Specifically, after accounting for dinucleotide biases, the proportion of codon usage bias explained by mutation pressure often increases, as seen in human RNA ... See full document
8
Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms
... this analysis, it does not perfectly re-capitulate the observed patterns of codon ...of codon usage at those sites ...in codon bias between genes due to gene-specific selective ... See full document
15
Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp
... (ENC), codon adaptation index (CAI), and correspondence analysis (COA) for each of the selected genetic data [9, ...cleotide composition analysis was conducted based on the overall frequency ... See full document
10
Codon bias of influenza a viruses and their hosts
... acid composition on codon usage calculation they incorporated the volatil- ity of codons, defined below, into the measurement of the codon ...each codon has nine possible single-nu- ... See full document
9
Analysis of synonymous codon usage in Hepatitis A virus
... higher codon usage bias than other members of the family? Furthermore, how does it form kinds of trends in codon usage variation among different stains (Shown in Figure 1) in the ... See full document
8
Analysis of Gene Expression using Modified Relative Codon Bias Strength in Nanoarchaeum Equitans
... compositional bias seen among these 25 codons which comprise 12 G/C and 13 A/T codons ending at third ...as codon usage bias indicator at ... See full document
7
Long-Term Evolution and Functional Diversification in the Members of the Nucleophosmin/Nucleoplasmin Family of Nuclear Chaperones
... Our analysis shows that there is extensive silent divergence at the nucleotide level suggesting that this family has been subject to strong purifying selection at the protein ...of codon bias ... See full document
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In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
... for analysis of selection operating on genes, Plotkin et ...[12]. Codon volatility measures the different number of mutations required for synonymous codons to be trans- formed into codons encoding a ... See full document
12
In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
... for analysis of selection operating on genes, Plotkin et ...[12]. Codon volatility measures the different number of mutations required for synonymous codons to be trans- formed into codons encoding a ... See full document
12
The Complete Mitochondrial Genome of the Damsel Bug Alloeorhynchus bakeri (Hemiptera: Nabidae)
... the nucleotide composition, codon usage, composi- tional biases, RNA secondary structure, and evaluate the phylogenetic position of Nabidae in Heteroptera based on the sequences of ... See full document
15
Nucleotide composition of the Zika virus RNA genome and its codon usage
... exotic codon usage employed by ...umented codon usage adaptation in pandemic ZIKV virus strains ...this bias usually coincides with a bias in nt-composition of the viral ... See full document
9
Genome wide analysis of codon usage bias in Bovine Coronavirus
... of codon usage bias in BCoV, the ENC ’ s values were calculated for the complete genome of all BCoV ...third codon pos- ition) was constructed. An ENC-GC3S plot of genes whose codon ... See full document
7
Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria
... our analysis of the evolu- tionary rates and patterns for various gene types among five Frankia, five Mycobacterium and five Streptomyces ...selection. Codon usage analysis of actinobacterial ... See full document
16
Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda
... Andolfatto, P., 2001 Contrasting patterns of X-linked and autoso- Marin, I., M. L. Siegal and B. S. Baker, 2000 The evolution of mal nucleotide variation in Drosophila melanogaster and Drosophila ... See full document
12
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] ... See full document
11
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] ... See full document
12
Selection at the Amino Acid Level Can Influence Synonymous Codon Usage: Implications for the Study of Codon Adaptation in Plastid Genes
... a nucleotide mutation accuracy on codon usage (Akashi 1994; Tautz and is “accepted” by ...the codon usage of conserved amino acid sites the probability of a nonsynonymous mutation being ... See full document
12
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K 12 genome
... determine codon usage are translational selection and mutational bias (7,8), and these factors can be called upon again to account for the trends in COA and expression levels observed in this ...the ... See full document
12
Characterizing the interplay between gene nucleotide composition bias and splicing
... ChIP-seq or MNase-seq datasets were recovered from Cistrome, ENCODE, and GEO databases (Add- itional file 1: Table S1). Coverage files (BigWig) were directly downloaded from Cistrome and RNAPII ChIP- seq from ENCODE. ... See full document
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SEQUENCE EVOLUTION OF DROSOPHILA MITOCHONDRIAL DNA
... Analysis of nucleotide substitutions in the third position of codons of two- codon and four-codon families of Drosophila mitochondrial protein genes re- vealed relat[r] ... See full document
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