How can I set threshold for amino acid site profile of type1 functional divergence implemented in DIVERGE 3.0 version?
I am analysing type 1 functional divergence of gene family consisting of four members. The result of type 1 functional divergence shows significant functional divergence (Ө>0 at P<0.01) among all the members. How can I set threshold (threshold for posterior probability) for prediction of acid residues of site based profile that are critical for subfamily specific functional divergence?
I used the following method for defining threshold for posterior probability, is it the correct one?
I consecutively deleted highest scoring residues until θ reached zero. The minimum probability of deleted residue at which theta reaches zero should be set as the threshold, e.g. when I deleted residues having probability >=75 then theta reached zero. Should I use 75% probability as threshold?
Thanks
