Predicting Most Diverged Genes From An Orthology Cluster

Question

[GR]

Dear All,

Between species A and B, I have the list of orthology clusters. Now from species B from a ortholog group, we want to know which of the gene is the most diverged one. Below is figure for an hypothetical orthology cluster:

Species A | Species B A1, A2 | B1, B2, B3, B4

Now if I have to answer which one is more diverged between B1, B2, B3 and B4, What would be the method?

Blast can only tell give you the homolog sequences. Can anyone suggest a better approach to answer this?

Thanks, RT

Answer 1

[5heikki]

If there are hmms for these genes you could just see which one differs the most from the model..

[GR]

do you mean by hidden markov model?

[5heikki]

Yeah, more specifically hmms from pfam.