Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias
نویسندگان
چکیده
منابع مشابه
Accounting for background nucleotide composition when measuring codon usage bias.
The phenomenon of codon usage bias has been important in the study of evolution because it provides examples of weak selection working at the molecular level. During the last two decades, evidence has accumulated that some examples of codon usage bias are driven by selection, particularly for species of fungi (e.g., Bennetzen and Hall 1982; Ikemura 1985), bacteria (e.g., Ikemura 1981; Sharp and...
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flaviviridae are viruses that cause several diseases including dengue fever, japanese encephalitis, murray valley encephalitis, tick-borne encephalitis, west nile encephalitis, yellow fever and hepatitis c virus infection. members of this family have monopartite, linear, single-stranded rna genomes of positive polarity, 9.6-12.3 kb in length. here, we have analyzed the codon usage of 13 species...
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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...
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O código genético é degenerado, isto é, o mesmo amino ácido pode ser codificado por vários codons. Apesar de codificarem o mesmo amino ácido, estes codons sinônimos não são utilizados da mesma forma em genomas diferentes, e mesmo em um único genoma o padrão de uso dos codons sinônimos pode variar muito entre os genes, ou ainda ao longo de um único gene. Com a recente introdução de seqüências ge...
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Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of ribosome protected mRNA fragments (Ribo-se...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2002
ISSN: 1537-1719,0737-4038
DOI: 10.1093/oxfordjournals.molbev.a004201