Quantifying Position-Dependent Codon Usage Bias
نویسندگان
چکیده
منابع مشابه
Quantifying Position-Dependent Codon Usage Bias
Although the mapping of codon to amino acid is conserved across nearly all species, the frequency at which synonymous codons are used varies both between organisms and between genes from the same organism. This variation affects diverse cellular processes including protein expression, regulation, and folding. Here, we mathematically model an additional layer of complexity and show that individu...
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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...
متن کاملA Model of Codon Usage Bias
Submitted for the MAR07 Meeting of The American Physical Society A Model of Codon Usage Bias MORTEN KLOSTER, CHAO TANG, UCSF — The genetic code is degenerate; most amino acids can be encoded by from two to as many as six different codons. While one might expect these codons to be used with equal frequency, this turns out not to be the case—not only are some codons favored over others, but their...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2014
ISSN: 1537-1719,0737-4038
DOI: 10.1093/molbev/msu126