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