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Table 1 Execution time performance for standard and Boolean USM implementations.

From: Efficient Boolean implementation of universal sequence maps (bUSM)

Length of
Sequence A
Length of
Sequence B
Total Time
(Boolean USM)
Distance Compute Time
(Boolean USM)
Total Time
(standard USM)
Distance Compute Time
(standard USM)
Rate (Boolean USM distance
calculations per second)
Rate (standard USM distance
calculations per second)
Speed Ratio
(Boolean to standard)
Memory (kB)
1,000 1,000 0.12 0.12 0.44 0.44 8,333,333 2,272,727 3.67 94
2,000 2,000 0.48 0.48 1.78 1.77 8,333,333 2,244,669 3.71 188
3,000 3,000 1.09 1.09 3.98 3.98 8,249,313 2,264,151 3.64 281
4,000 4,000 1.92 1.92 7.08 7.08 8,324,662 2,259,887 3.68 375
5,000 5,000 3.04 3.03 11.07 11.07 8,212,878 2,259,376 3.64 469
10,000 10,000 30.53 30.52 58.17 58.16 3,275,145 1,719,011 1.91 938
15,000 15,000 68.68 68.67 131.01 131.00 3,276,158 1,717,452 1.91 1,406
17,000 17,000 88.23 88.21 168.29 168.28 3,275,678 1,717,253 1.91 1,594
20,000 20,000 122.09 122.07 233.00 232.99 3,276,406 1,716,775 1.91 1,875
40,000 40,000 488.46 488.43 931.74 931.71 3,275,587 1,717,219 1.91 3,750
  1. Results of performance comparisons of standard USM and Boolean USM implementations in C (gcc 2.95.3, cygwin, Windows 2000, PIII 1 GHz). Sequence lengths are given in nucleotides. Times measure elapsed execution time in seconds. Total times include both USM sequence preparation time and distance calculations for all symbol pairs. Memory is measured in kilobytes and represents the space required to store the USM coordinates for both sequences.