I am relativly new to the field and I am dealing now with the codon usage for different proteins in several pathways to see if there is corelation. Just to be sure about the metod - As I would like to compare two different organism I would like to set the reference codon usage table of the whole genome, and then calculate CAI for each gene in each organism. Will I be than able to relevantly compare CAI from homologous genes?
Thank you very much for your answers! Martin Kavšček