How to quantify gaps in multiple sequence alignments
Consider a trivially small multiple sequence alignment (MSA) of four peptides:
AAAA
-AAA
--AA
---A
I quantify gaps along the "x" axis, by simply stating what fraction of proteins are present/defined at that position. The small MSA above, would have values of 1,2,3,4. I call this "mean # of proteins" or "mean protein presence".
My explanation of this metric is confusing other people.
Is there a more commonly accepted metric that would explain this concept more simply? and be less confusing to others?
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Isn't this usually looked at the "other way around" in terms of the column occupancy (http://prody.csb.pitt.edu/tutorials/evol_tutorial/msaanalysis.html)?