I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE.
- I would like to ask if consistency score plays any role in the interpretation?
- I would like to ask for a region of a protein to be considered conserved, all the amino acids should have similar properties? So even if only one protein has a different amino acid (among the proteins that are included in the multiple alignment), then there is no conservation? for example, in this picture,
- I am curious why there is no dot beneath some columns with almost identical amino acids (expect one sequence for example).