Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila
نویسندگان
چکیده
منابع مشابه
Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.
We present a likelihood method for estimating codon usage bias parameters along the lineages of a phylogeny. The method is an extension of the classical codon-based models used for estimating dN/dS ratios along the lineages of a phylogeny. However, we add one extra parameter for each lineage: the selection coefficient for optimal codon usage (S), allowing joint maximum likelihood estimation of ...
متن کاملSCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation
The genetic code is degenerate--most amino acids can be encoded by from two to as many as six different codons. The synonymous codons are not used with equal frequency: not only are some codons favored over others, but also their usage can vary significantly from species to species and between different genes in the same organism. Known causes of codon bias include differences in mutation rates...
متن کاملMaximum Likelihood Estimation of Parameters in Generalized Functional Linear Model
Sometimes, in practice, data are a function of another variable, which is called functional data. If the scalar response variable is categorical or discrete, and the covariates are functional, then a generalized functional linear model is used to analyze this type of data. In this paper, a truncated generalized functional linear model is studied and a maximum likelihood approach is used to esti...
متن کاملEvolution of codon usage bias in Drosophila.
We first review what is known about patterns of codon usage bias in Drosophila and make the following points: (i) Drosophila genes are as biased or more biased than those in microorganisms. (ii) The level of bias of genes and even the particular pattern of codon bias can remain phylogenetically invariant for very long periods of evolution. (iii) However, some genes, even very tightly linked gen...
متن کاملMore Codon Usage Bias
χ measure. In statistics, the χ statstic computes how different the distribution of values is from a uniform distribution. Let d = c1 . . . cN be a DNA string in nucleotide alphabet, and let L be the total number of codons in d that are not Methinine or Tryptophan (the number does include the stop codons though). Let a be a k-degenerate amino acid, and let La be the total number of codons codin...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2006
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/msl146