Table 1 Speed of genomic search and space usage
From: Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays
Reverse search | Forward search | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
SA | CSA-Sada | SA-WT | CSA-WT | SA | ESA | ESA-bp | ESA-byte | ESA-gdi | ||
Space used (bytes per genome length) | ||||||||||
Fly | 3.5 | 0.9 | 4.9 | 0.9 | 3.5 | 11.4 | 8.0 | 6.6 | 7.1 | |
Chick | 3.8 | 1.0 | 5.1 | 0.9 | 3.8 | 11.9 | 8.5 | 6.3 | 6.8 | |
Human | 4.0 | 1.0 | 5.5 | 0.9 | 4.0 | 12.4 | 9.0 | 7.1 | 7.6 | |
Counting task (microseconds per query) | ||||||||||
Fly | 12-mers | 42.9 | 45.6 | 1.6 | 1.7 | 46.8 | 2.3 | 52.6 | 5.2 | 1.7 |
24-mers | 81.5 | 88.8 | 4.7 | 4.8 | 47.6 | 2.5 | 54.0 | 5.3 | 2.1 | |
36-mers | 119.1 | 130.0 | 5.9 | 7.0 | 42.5 | 2.8 | 54.6 | 5.6 | 2.2 | |
Chick | 12-mers | 52.4 | 44.5 | 2.0 | 2.1 | 54.7 | 2.8 | 61.4 | 7.3 | 2.3 |
24-mers | 98.0 | 90.3 | 4.5 | 5.3 | 53.5 | 3.6 | 65.7 | 8.7 | 3.0 | |
36-mers | 148.1 | 137.4 | 9.0 | 8.2 | 54.5 | 3.8 | 67.1 | 7.9 | 3.3 | |
Human | 12-mers | 59.8 | 49.3 | 2.4 | 2.7 | 58.4 | 3.4 | 75.0 | 10.0 | 3.1 |
24-mers | 101.5 | 94.5 | 5.8 | 5.6 | 66.8 | 5.1 | 76.7 | 12.1 | 4.0 | |
36-mers | 151.0 | 139.3 | 9.3 | 9.4 | 70.2 | 5.2 | 81.1 | 11.9 | 4.0 | |
Locating task (microseconds per query) | ||||||||||
Fly | 12-mers | 49.6 | 223.8 | 21.5 | 147.8 | 52.0 | 3.5 | 52.2 | 6.7 | 2.9 |
24-mers | 86.5 | 135.0 | 12.0 | 45.2 | 47.4 | 3.1 | 53.9 | 5.5 | 2.5 | |
36-mers | 130.2 | 157.6 | 12.9 | 32.1 | 51.3 | 3.1 | 59.3 | 6.5 | 2.4 | |
Chick | 12-mers | 62.0 | 682.7 | 45.8 | 628.3 | 61.5 | 5.2 | 63.9 | 10.7 | 4.3 |
24-mers | 104.5 | 102.9 | 7.2 | 16.3 | 54.2 | 4.0 | 64.1 | 7.9 | 2.8 | |
36-mers | 141.0 | 134.5 | 8.8 | 13.5 | 51.7 | 3.8 | 65.6 | 7.7 | 3.3 | |
Human | 12-mers | 80.1 | 6300.8 | 602.6 | 5798.1 | 99.0 | 30.4 | 94.1 | 37.6 | 28.5 |
24-mers | 101.4 | 393.6 | 40.8 | 264.0 | 68.1 | 6.8 | 77.4 | 13.8 | 5.5 | |
36-mers | 149.7 | 175.8 | 12.6 | 46.1 | 60.0 | 5.1 | 79.3 | 12.7 | 4.3 | |
Locating task (nanoseconds per match result) | ||||||||||
Fly | 12-mers | 69.2 | 312.4 | 30.1 | 206.2 | 72.5 | 4.8 | 72.9 | 9.3 | 4.1 |
24-mers | 360.5 | 562.8 | 50.2 | 188.6 | 197.8 | 13.0 | 224.6 | 23.1 | 10.3 | |
36-mers | 941.9 | 1140.1 | 93.8 | 232.7 | 371.5 | 22.8 | 429.3 | 47.0 | 17.3 | |
Chick | 12-mers | 36.7 | 404.1 | 27.1 | 371.9 | 36.4 | 3.1 | 37.8 | 6.3 | 2.5 |
24-mers | 2993.0 | 2948.3 | 206.9 | 467.4 | 1551.5 | 115.8 | 1836.9 | 226.7 | 81.5 | |
36-mers | 9723.0 | 9274.2 | 606.4 | 928.8 | 3566.7 | 259.6 | 4527.3 | 533.2 | 226.3 | |
Human | 12-mers | 3.3 | 259.9 | 24.9 | 239.1 | 4.1 | 1.3 | 3.9 | 1.6 | 1.2 |
24-mers | 71.0 | 275.6 | 28.6 | 184.8 | 47.7 | 4.7 | 54.2 | 9.7 | 3.9 | |
36-mers | 800.8 | 940.7 | 67.7 | 246.5 | 320.8 | 27.3 | 424.5 | 68.2 | 23.2 | |