The pair-wise sequence alignment algorithms outlined in the previous
sections are guaranteed to produce a mathematically optimal
alignment for two sequences given the chosen pair-score matrix
(e.g. BLOSUM62) and gap-penalty function. However, the fact that an
alignment is optimal for the matrix and penalty, does not mean that
the alignment is biologically or structurally meaningful. One can
take any two sequences and optimally align them, but an optimal
alignment of, say, a globin (an all-