[PDF] Top 20 Estimating Selection on Nonsynonymous Mutations
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Estimating Selection on Nonsynonymous Mutations
... deleterious, nonsynonymous mutations, using polymorphism data from two related ...nonneutral mutations is given by the value under mutation-selection balance, while the second method allows ... See full document
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The Correlation Between Synonymous and Nonsynonymous Substitutions in Drosophila: Mutation, Selection or Relaxed Constraints?
... that selection ing regions of 250 codons with a G 1 C content of ...both selection coeffi- cients on synonymous (s s ) and nonsynonymous (s a ) ... See full document
9
Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations
... deleterious mutations. In the typical population genetic approach for estimating the DFE, the population demography is first inferred using a putatively neutral class of mutations, and the DFE for ... See full document
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The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory
... ing mutations: Several results regarding the ages of neu- and Kaplan ...tral mutations are ...However, selection will affect the expected coalescence time of a sample of size 2 the underlying gene ... See full document
10
γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates
... estimate nonsynonymous and synonymous substitution rates for interrogating sequence dynamics and constructing phylogenetic ...per nonsynonymous and synonymous site, respectively, these parameters (or often ... See full document
18
Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations
... mtDNA mutations A total of 5920 single base mutations from 3277 patients of 26 tumor types (Additional file 1: Figure S1) were collected from two databases (TCGA and ICGC), three previous publications, and ... See full document
12
The Evolution of Selfing Is Accompanied by Reduced Efficacy of Selection and Purging of Deleterious Mutations
... deleterious mutations that accumulated in eight randomly sampled indi- ...of nonsynonymous mutations that were present once was 1 2 ...all mutations in their ... See full document
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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
... for estimating the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of ... See full document
12
Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster
... these mutations 10 times more likely to be purged by natural selection than nonsynonymous ...purifying selection would radically reduce any impact of de novo duplication and deletion rates on ... See full document
25
Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes
... constant selection for nucleotide usage, we would expect to find differences between the nucleotide substitution matrices inferred from internal ver- sus external ...eterious mutations, and the largely ... See full document
8
Population Genetics of Polymorphism and Divergence for Diploid Selection Models With Arbitrary Dominance
... for estimating both selection and dominance parameters of new mutations using information on the frequency spectrum of sequence ...genic selection; simulations indicate that this test is quite ... See full document
14
A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL
... deleterious mutations can explain this rate ...of nonsynonymous substitution rates across Buchnera species are strikingly low at groEL compared to other ...purifying selection on groEL, our ... See full document
10
Selection at the Amino Acid Level Can Influence Synonymous Codon Usage: Implications for the Study of Codon Adaptation in Plastid Genes
... of selection for translation amino acid j that is generated by a nucleotide mutation accuracy on codon usage (Akashi 1994; Tautz and is “accepted” by ...a nonsynonymous mutation being with those that vary ... See full document
12
Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
... which mutations are common in the naturally occurring ...on estimating the P- value (or posterior probability) of ω > 1 rather than the numerical value of ω ... See full document
24
Functional relevance of nonsynonymous mutations in the HIV 1 tat gene within an epidemiologically linked transmission cohort
... of mutations in the HIV-1 tat gene within an epidemiologically-linked AIDS transmission cohort consisting of a non-progressing donor (A) and two normal progressing recipients (B and ...Multiple ... See full document
5
Significance of Population Size on the Fixation of Nonsynonymous Mutations in Genes Under Varying Levels of Selection Pressure
... A previous study showed a large difference between v estimated for primates and rodents using the amino acid sites that are conserved or necessary for the structure and/ or function of protein (Subramanian 2011). In ... See full document
8
The Amino-Acid Mutational Spectrum of Human Genetic Disease
... of selection. (b) The nonsynonymous benign SNP frequencies using the SNP dataset of Stephens et ...the mutations close to the matrix diagonal tend to be more ... See full document
11
Mutations as Missing Data: Inferences on the Ages and Distributions of Nonsynonymous and Synonymous Mutations
... of nonsynonymous and synon- the new MCMC method for these models will be faster ymous substitutions in internal ...treat mutations as missing also can be performed directly as a likelihood-ratio test ...the ... See full document
11
Estimating the evidence of selection and the reliability of inference in unigenic evolution
... codon-triplet mutations were ...and nonsynonymous mutation counts alone have sufficient power to resolve functional versus nonfunctional ...nonymous mutations at a particular site in both the ... See full document
24
Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples
... of selection coefficients of new mutations under the PRF model using the ...of selection coefficients and saves each SFS into an ...each selection coefficient in each step of the optimization ... See full document
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