Up till now, we have assumed that all codons coding for the same amino acid are interchangeable. In fact, this not entirely true. In many species, it...

I'm confused about how to know which one is more efficient

Up till now, we have assumed that all codons coding for the same amino acid are interchangeable. In fact,this not entirely true. In many species, it has been observed that certain codons are (slightly) favored. This iscalled codon bias. For example, AAA and AAG both code for lysine. If, in a particular species, the AAA codon is used preferentially, we would call that codon bias. One source of codon bias has to do with the efficiency of the transcriptional machinery. It is thought thatfavored codons can allow the transcriptional machinery to work more smoothly. This effect however, variesbetween species. A. The impact of codon bias on gene finding.Consider three cases. Case 1. We take a well studied species with good gene annotations (species A) and build a Markov model oncodons. We then use this model to find genes in the closely related species B. These two species have littleor no codon bias. Case 2. We take a well studied species with good gene annotations (species C) and build a Markov model oncodons. We then use this model to find genes in the closely related species D. Species C and D each havestrong codon bias, however the biases in the two species are different. (Taking the lysine example to illustrate, in one species the AAA codon is favored, but in the other the AAG is.) Case 3. We take a well studied species with good gene annotations (species E) and build a Markov model oncodons. We then use this model to find genes in the closely related species F. Species E and F have strong codon bias which is the same in both species. (e.g. in the lysine example both favor AAA). Rank these three cases in terms of how effective you would expect the gene finder to be. (Effectiveness for the gene finder means having a high true positive rate and low false discovery rate.) Explain your reasoning.