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CHIPS application details page
Codon usage statistics
chips calculates Frank Wright's Nc statistic for the effectivenumber of codons used (ref 1). This is a simple measure that quantifies how far the codon usage of agene departs from equal usage of synonymous codons. This measure ofsynonymous codon usage bias, the 'effective number of codons used in agene', Nc, can be easily calculated from codon usage data alone, and isindependent of gene length and amino acid (aa) composition. Nc can takevalues from 20, in the case of extreme bias where one codon isexclusively used for each aa, to 61 when the use of alternativesynonymous codons is equally likely. Nc thus provides an intuitivelymeaningful measure of the extent of codon preference in a gene. The Nc statistic has problems in very short sequences (20 amino acidsor less) which are yet to be fully resolved. They are caused by theneed to consider amino acids which are missing in the sequence. This calculation was originally in the EGCG package as "codfish"(codon usage for fission yeast). As Frank Wright is a vegan, we lookedfor a meat-free name for the EMBOSS version, "chips". The officialexplanation is "Codon Heterozygosity (Inverse of) in aProtein-coding Sequence" If the sequence extends beyond the coding region then the start and/orend positions of the CDS must be provided because chips analysesexclusively protein coding regions.
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