CodonAdaptationIndexInterface
in
Interface CodonAdaptationIndexInterface - scores how well a coding sequence's own codon choices match a reference organism's preferred codons (Sharp & Li, 1987), useful for predicting or optimizing how well a cloned insert is likely to express in a given host.
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Table of Contents
Methods
Methods
calculate()
public
calculate(DnaSequence $oCodingSequence, CodonUsageTable $oReferenceTable[, int $iGeneticCode = 1 ]) : CaiResult
Parameters
- $oCodingSequence : DnaSequence
-
A CDS, in frame from its first base ; only complete trailing codons are considered
- $oReferenceTable : CodonUsageTable
-
The host organism's reference codon usage
- $iGeneticCode : int = 1
-
An NCBI genetic code table id, 1 (standard) by default