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. 2008 Jun 27;36(13):4286–4294. doi: 10.1093/nar/gkn390

Table 1.

Successive performance improvement of PIPE to PIPE2. Using all improvements PIPE2 now runs more than 16 000 times faster than the original PIPE

Version Average Runtime (s) Speedup
Original PIPE implementation 6944.40
+Digital alphabet optimization 389.65 18×
+Sliding window optimization 160.53 43×
+Pre-computation/Query approach (PIPE-2) 0.43 16 150×