Entering edit mode
7.5 years ago
bordin89
•
0
Hi! I have two datasets of proteins, each of them is a collection of clusterized proteins obtained using OrthoMCL. What I'd like to know is this: If I make a MSA among the members of each cluster in each dataset, can I infer from them (by making an average between all the clusters) if dataset A evolved faster or slower in comparison with dataset B? How would you do it? I was reading on a review that the alignment percentage could be a good metric, but is it true?
The dN/dS ratios are usually used if you want to see any selection. This is recommended with 4 or more protein sets but you can also use 3 (less power). This can be done with 3rd protein as an outgroup, then check if selection acts on the branch of two proteins you are interested in through branch models, this is what PAML is for. If you see a different rate in your selected branch then you can check further if there is a positive or negative selection through branch-site models. This could be a nice place to start