CodonOptimizerInterface
in
Interface CodonOptimizerInterface - the inverse of CodonAdaptationIndexCalculator : rather than scoring an existing coding sequence against a reference codon usage table, this picks, for each residue of a target protein, the synonymous codon with the highest count in that table - the coding sequence a perfect (CAI = 1) translation of the protein would have.
Tags
Table of Contents
Methods
Methods
optimize()
public
optimize(AminoAcidSequence $oProtein, CodonUsageTable $oReferenceTable[, int $iGeneticCode = 1 ]) : DnaSequence
Parameters
- $oProtein : AminoAcidSequence
-
May include a trailing "*" for a stop
- $oReferenceTable : CodonUsageTable
- $iGeneticCode : int = 1
-
An NCBI genetic code table id, 1 (standard) by default