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Synonymous substitution rates in enterobacteria.
... The decline in the substitution rate across gene ex- pression levels appears to be independent of selection in favor of synonymous codon bias; amino acids such as LYS, whic[r] ... See full document
6
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
... and synonymous substitution rates for interrogating sequence dynamics and constructing phylogenetic ...and synonymous site, respectively, these parameters (or often their ratio Ka/Ks or Z) are ... See full document
18
Role of viral evolutionary rate in HIV 1 disease progression in a linked cohort
... non-synonymous/synonymous substitution rate ratio scan was performed on the com- plete genomes using a maximum likelihood estimation procedure (Figure ...heterogeneous rates along sequences, ... See full document
10
The Causes of Synonymous Rate Variation in the Rodent Genome: Can Substitution Rates Be Used to Estimate the Sex Bias in Mutation Rate?
... neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) ...usage, synonymous rates, and nonsynony- mous rates suggest that silent sites in rodents are evolving ... See full document
14
Rapid Evolution of Mammalian X-Linked Testis-Expressed Homeobox Genes
... inferred ancestral TGIFLX sequences at all interior nodes of Retroposition is a mutation-prone process due to a high this tree, using the distance-based Bayesian method (Zhang error rate in retrotranscription. Also, ... See full document
10
The Effect of Tandem Substitutions on the Correlation Between Synonymous and Nonsynonymous Rates in Rodents
... Simulated substitution sequences were generated under the tein-coding sequence available in a single GenBank/EMBL assumption of independent ...nonsynonymous substitution rates of the real se- HGMP ... See full document
8
Different rates of (non )synonymous mutations in astrovirus genes; correlation with gene function
... sequences involved has pointed out that the sequences of turkey species have been determined by RT-PCR of virus RNA extracted directly from stools and organs [18,29], whereas RNAs of avian nephritis virus have been ... See full document
12
Explorations of Site-to-Site Synonymous Substitution Rate Variability.
... the synonymous substitution rate across sites is constant and thus attributes any variation in the overall ω rate to nonsynonymous rate variation ...the synonymous and nonsynonymous ... See full document
157
Estimating divergence dates and substitution rates in the Drosophila phylogeny.
... (i.e., substitution at less than the neutral rate at some synonymous ...by substitution saturation of 4-fold sites (supplementary ...relative rates of evolution at different sites (model ... See full document
15
Complete Chloroplast Genome Sequences of Clematis: IR Expansion and Relative Rates of Synonymous Substitutions
... Gene contents in the complete chloroplast genomes of these two Clematis species are.. 15.[r] ... See full document
12
Synonymous Rates at the RpII215 Gene of Drosophila: Variation Among Species and Across the Coding Region
... of synonymous substitutions detected in the ...if synonymous mutations behave as nearly ...for synonymous and nonsynonymous substitutions was detected when comparing the ...and synonymous ... See full document
12
Substitution Rates in Drosophila Nuclear Genes: Implications for Translational Selection
... and enterobacteria, synonymous substitutions appear to bination (Kliman and Hey 1994; Comeron et ...ila, synonymous codon usage is highly biased toward other selected sites (Hill and Robertson ... See full document
11
Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses
... of synonymous substitutions of the codon site at which the nucleotide is ...Low synonymous substitution rates are observable in the stem region in all data sets, indicating that there is a ... See full document
18
Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response
... higher rates of non-synonymous mutations detected in NR patients may indicate an advantage in evading both the immune system and the treatment, since they may be able to modify epitopes so that they are no ... See full document
9
Rates of synonymous substitution and base composition of nuclear genes in Drosophila.
... Because the synonymous substitution for functional genes and the nucleotide substitution for pseudogenes are exempted from any selective constraint at the protein lev[r] ... See full document
10
The Problem of Counting Sites in the Estimation of the Synonymous and Nonsynonymous Substitution Rates: Implications for the Correlation Between the Synonymous Substitution Rate and Codon Usage Bias
... different substitution rate to ...different rates while the number of tially that of Li (1993) and Pamilo and Bianchi (1993) sites is calculated assuming that transitions and transver- but with one small ... See full document
12
Variable rates of evolution among Drosophila opsin genes.
... Rates and patterns of nucleotide substitution are compared among the different opsin loci, and two factors that are thought to affect rates of synonymous nucleotide sub[r] ... See full document
12
Origin and Evolution of a Chimeric Fusion Gene in Drosophila subobscura, D. madeirensis and D. guanche
... and synonymous changes are beneath the branches of the Adh -Twain ...the rates of amino acid substitution, but not synonymous substitutions, relative to the ancestral ... See full document
14
Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution: Approximate and Maximum-Likelihood Methods Lead to Different Conclusions
... of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous ...estimate rates of ... See full document
10
Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection
... of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are ...lower rates of synonymous substitutions, and ... See full document
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