Question: Predicting Most Diverged Genes From An Orthology Cluster
gravatar for RT
7.3 years ago by
European Union
RT350 wrote:

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

ADD COMMENTlink modified 7.3 years ago by 5heikki9.3k • written 7.3 years ago by RT350
gravatar for 5heikki
7.3 years ago by
5heikki9.3k wrote:

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

ADD COMMENTlink written 7.3 years ago by 5heikki9.3k

do you mean by hidden markov model?

ADD REPLYlink written 7.3 years ago by RT350

Yeah, more specifically hmms from pfam.

ADD REPLYlink written 7.2 years ago by 5heikki9.3k
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