Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
نویسندگان
چکیده
منابع مشابه
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the patt...
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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...
متن کاملRelative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon usage table trained with a set of highly expr...
متن کاملCodon adaptation index as a measure of dominating codon bias
UNLABELLED We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias. With the set of coding sequences as a...
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: BMC Bioinformatics
سال: 2012
ISSN: 1471-2105
DOI: 10.1186/1471-2105-13-43