“The execution time required for a gapped extension is ~500
times that for an ungapped extension. However, by triggering
gapped extensions in the manner described, while simultaneously
raising T for the single-hit version of BLAST from 11 to 13,
approximately one gapped extension is invoked for every 4000
ungapped extensions avoided. Because the number of ungapped
extensions is reduced by about two thirds, the total time spent on
the extension stage of BLAST is cut by well over half. Of course,
the two-hit strategy described above reduces the time needed for
the ungapped extensions still further. Once program overhead is
accounted for, the net speedup is a factor of about three.”