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Table 1 Speed of genomic search and space usage

From: Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays

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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
  1. Genome sources: Drosophila melanogaster version 5.25.64 (Fly), Gallus gallus gg4 (Chick), and Homo sapiens hg19 (Human)
  2. SA uncompressed suffix array; CSA-Sada compressed suffix array using Sadakane method; SA-WT and CSA-WT uncompressed and compressed suffix array, respectively, using wavelet tree. ESA enhanced suffix array, ESA-bp ESA with balanced parenthesis representation; ESA-byte ESA with bytecoding; ESA-gdi ESA with exception guide arrays, discriminating character array, and integrated data structure