I found the homology ratio* 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.
As the topic of homology analysis is non that trivial, I have a couple of questions:
- Can we compare the ratio of homology between the above 2 couples or such a comparison is biased - non scientific and why(even though I have seen studies where the ratio of homology found between different organisms and an organism of reference are compared)?
- Shouldn't the ratio of homology be proportional to the evolutionary distance of the organisms (according to conservation)?
I am looking for an article/research that clarifies the matter but cannot really find one!
Thanks in advance for any suggestions!
*When I am talking about homology ratio above, I mean protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism. x 100 :-)
The way I calculate the above ratio, I dont take into acount the one-to-many or many-to many relationships! I just find the genes that have at least one homolog in mouse..i think that might be the bias of my calculation, right?