An Upper Bound on the Convergence Rate of a Second Functional in Optimal Sequence Alignment

Raphael Hauser, Heinrich Matzinger, Ionel Popescu

Consider finite sequences $X_{[1,n]}=X_1\dots X_n$ and $Y_{[1,n]}=Y_1\dots Y_n$ of length $n$, consisting of i.i.d.\ samples of random letters from a finite alphabet, and let $S$ a…