CodonWeightTable {SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.DeltaSimilarity1998.CAI}

.NET clr documentation

CodonWeightTable

Description

CODON ADAPTATION INDEX (CAI, Sharp & Li) weight table.

This specifies a reference set of genes, H, chosen from among "highly expressed genes". Defining

    w(codon) = f^H(codon) / max_{synonyms} f^H(.)

as the ratio of the frequency of the codon to the maximal codon frequency in H for the same amino acid, the CAI of a gene of length L is taken as

    CAI(gene) = (w1 * w2 * ... * wL)^(1/L)

(the geometric mean, computed numerically through the log-average).

This is a two-step API: first build the w table from the reference gene set H (this class), then evaluate the target genes (see CodonAdaptationIndexEvaluation.CAI()).

(compatible rename of the legacy RelativeCodonBiases class, which mistakenly used each single ORF as its own reference set and thus always produced CAI values close to 1)

Declare

            
# namespace SMRUCC.genomics.Analysis.SequenceTools.DNA_Comparative.DeltaSimilarity1998.CAI
export class CodonWeightTable {
   GeneticCode: GeneticCodes;
   # the display name of the reference gene set H
   Name: string;
   # Pseudocount assigned to the codons which are absent in the reference set H, expressed as an absolute count. Prevents the geometric mean from being zeroed out by a single unused codon.
   PseudoCount: double;
   # Total number of sense codons counted in the reference set H.
   TotalCodons: integer;
}

        

.NET clr type reference tree

1. use by property member GeneticCode: GeneticCodes

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