Basically if I have binary sequence that I want to check against, and I want to determine how far other binary sequences are to this first sequence, what is the most appropriate measure to use.
The distance measures i have seen, like Manhattan etc., all give numeric values indicating ultimately the difference, not how far one sequence is from another.
For example -
A - 0101000010
B - 0000000010
C - 0101000000
D - 0000000100
C is much closer in similarity to A, than B is. I want a measure that calculates a percentage of the relative distances between all the values seen. The distance measures would score B and D the same - I want to show that D is actually further in similarity than B, and that C is the closest.
I have tried SOkal-SneathIV and other distance measures from "A Survey of Binary SImilarity and Distance Measures", 2009 - however for the sequences which have the same mismatches (regardless of position) end up with the same score - whereas I want the position reflected in the measure.