what is the best method to find a conserve amino acid ? and how can I validate it

Question

[Learner]

I know that there are plenty techniques which can be used for alignment. I want to know if any particular method is preferred? if so, which method? and how can one validate its results?

Answer 1

[Carlo Yague]

I want to know if any particular method is preferred? if so, which method?

Clustal is a good start for sequence alignment. But if the structure of your protein is available, a structural alignment might be worth looking into.

and how can one validate its results?

If you can, mutate the residue and check the activity of the protein. Usually, conserved amino acid are conserved because they are important for the protein function.