While BLAST is faster than any Smith-Waterman implementation for most cases, it cannot "guarantee the optimal alignments of the query and database sequences" as Smith-Waterman algorithm does.
Iako je BLAST brži od svih Smith-Waterman implementacija za većinu slučajeva, on ipak ne može da "garantuje optimalno poravnanje upita sa bazom sekvenci" kao Smith-Waterman algoritam.