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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?

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  • $\begingroup$ You want to compare the homology of proteins between species? To do so, see how phylogenetic trees are built. $\endgroup$ – Chris Mar 25 '15 at 13:47
  • $\begingroup$ There is the path of gene trees and species trees though! I am checking genes so i should care about the gene trees,correct? For example : It is very possible that in my analysis of gene X, species A is closest to mouse, while for gene Y species B is closest to mouse and that's where a bias is introduced! $\endgroup$ – NEWSCIENT Mar 25 '15 at 14:05
  • $\begingroup$ I don't understand your example, sorry. $\endgroup$ – Chris Mar 25 '15 at 14:16
  • $\begingroup$ Phylogenetic trees are usually much more complicated statistically/mathematically than simply ranking based on coding DNA homologies. Not going into the details (because I don't know enough about it) but in essence they try to reconstruct the best fitting tree amongst multiple organisms taking in account effects such as horizontal gene transfers and sequence conservations. Bottom line it is not a simple pairwise comparison between two organisms coding sequences and I am not too surprise you see an organism being closer than you would expect. My advice to you is trust the phylogenetic tree. $\endgroup$ – cagliari2005 Mar 26 '15 at 1:25
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1.Is such an approach trying to quantify homology? Which i know is not correct as homology is qualitive measure.

A common approach to identify orthologs (homology between two genes resulting from a speciation event) it 'best bidirectional match': if you blast gene A (in species 1) against all genes of species 2 the best match is gene B, and if you blast gene B against all genes of species 1 the best match is gene A.

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)?

Not necessarly. The fact that two genes diverged a very long time ago does not prevent them from being homologous. Homology is about shared ancestry (here of two genes) and not about evolutionary distance.

Could you clarify how you get the homologies? Did you compute them yourself (if so how) or did you use a specific database?

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