This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Predicting Most Diverged Genes From An Orthology Cluster

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

• 2,639 views • link
updated by 5heikki 5heikki • written by GR GR

1 answer

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

• 0 views • link
written by 5heikki 5heikki

do you mean by hidden markov model?

• 0 views • link
written by GR GR

Yeah, more specifically hmms from pfam.

• 0 views • link
written by 5heikki 5heikki

Log in to answer this question.

More posts like this