I found the following homology ratio:
protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism
I have done this for all protein coding genes between several organisms and mouse using a phylogenetic-based approach. I have noticed that the ratio found between an organism and mouse is greater than the ratio between another organism and mouse! On the other hand the second is evolutionary closer to mouse than the first.So:
1.Is such an approach trying to quantify homology? Which i know is not correct as homology is qualitive measure.
2.Can we compare the ratio of homology between the above 2 couples od species or such a comparison is biased?
3.Shouldn't the ratio of homology be proportional to the evolutionary distance of the organisms (according to conservation)?
As you can understand, in the way i calculate the above ratio, i don't take into account the one-to-many or many-to many relationships! I just take into account the genes that have at least one homolog in mouse..is that the bias of my calculation?