#gsa-is
This code is an implementation of gSAIS and gSACA-K, which are modifications of SAIS [1] and SACA-K [2] algorithms to compute the generalized suffix array, maintaining their theoretical bounds and improving their practical performance
-- Settings:
We have implemented six MODEs in main.c:
- 1: SAIS*
- 2: SACA-K*
- 3: SAIS
- 4: SACA-K
- 5: gSAIS
- 6: gSACA-K
* uses integer alphabet as input.
-- ##run:
To run a test type:
make
make run DIR=dataset INPUT=uniprot.100.fasta K=100 MODE=6##Experimental results
Collections:
| Collection | size (GiB) | d | n | n/d |
|---|---|---|---|---|
| Revision | 0.39 | 20,433 | 419,437,293 | 20,527 |
| Page | 3.74 | 1,000 | 4,019,585,128 | 4,019,585 |
| Influenza | 0.56 | 394,217 | 597,471,768 | 1,516 |
| Enwiki | 8.32 | 3,903,703 | 8,933,518,792 | 2,288 |
| DNA reads | 2.87 | 32,621,862 | 3,082,739,100 | 94 |
| Uniprot | 15.77 | 50,825,784 | 16,931,428,229 | 333 |
Datasets:
| Dataset | d | n | size (MiB) | avgLen |
|---|---|---|---|---|
| pages 1 | 2 | 2,371,241 | 2.26 | 1,185,621 |
| pages 2 | 7 | 14,707,622 | 14.03 | 2,101,089 |
| pages 3 | 15 | 35,043,296 | 33.42 | 2,336,220 |
| pages 4 | 31 | 52,890,374 | 50.44 | 1,706,141 |
| pages 5 | 62 | 119,466,260 | 113.93 | 1,926,875 |
| pages 6 | 125 | 412,148,014 | 393.05 | 3,297,184 |
| pages 7 | 250 | 840,886,051 | 801.93 | 3,363,544 |
| pages 8 | 450 | 2,127,332,977 | 2,028.78 | 4,727,407 |
| pages 9 | 650 | 2,635,913,891 | 2,513.80 | 4,055,252 |
| pages 10 | 1,000 | 4,019,585,128 | 3,833.38 | 4,019,585 |
| revesion 1 | 40 | 99,138 | 0.09 | 2,478 |
| revesion 2 | 80 | 260,366 | 0.25 | 3,255 |
| revesion 3 | 159 | 914,542 | 0.87 | 5,752 |
| revesion 4 | 319 | 2,091,943 | 2.00 | 6,558 |
| revesion 5 | 638 | 4,294,715 | 4.10 | 6,732 |
| revesion 6 | 1,277 | 16,058,904 | 15.31 | 12,575 |
| revesion 7 | 2,554 | 34,168,931 | 32.59 | 13,379 |
| revesion 8 | 5,108 | 59,888,778 | 57.11 | 11,725 |
| revesion 9 | 10,217 | 144,241,776 | 137.56 | 14,118 |
| revesion 10 | 20,433 | 419,437,293 | 400.01 | 20,527 |
| influenza 1 | 769 | 924,268 | 0.88 | 1,202 |
| influenza 2 | 1,539 | 1,773,953 | 1.69 | 1,153 |
| influenza 3 | 3,079 | 3,600,436 | 3.43 | 1,169 |
| influenza 4 | 6,159 | 7,056,864 | 6.73 | 1,146 |
| influenza 5 | 12,319 | 14,100,766 | 13.45 | 1,145 |
| influenza 6 | 24,638 | 32,959,239 | 31.43 | 1,338 |
| influenza 7 | 49,277 | 70,800,914 | 67.52 | 1,437 |
| influenza 8 | 98,554 | 142,930,737 | 136.31 | 1,450 |
| influenza 9 | 197,108 | 289,558,572 | 276.14 | 1,469 |
| influenza 10 | 394,217 | 597,471,768 | 569.79 | 1,516 |
| wikipedia 1 | 7,624 | 13,303,449 | 12.69 | 1,745 |
| wikipedia 2 | 15,248 | 25,737,808 | 24.55 | 1,688 |
| wikipedia 3 | 30,497 | 53,002,468 | 50.55 | 1,738 |
| wikipedia 4 | 60,995 | 101,073,689 | 96.39 | 1,657 |
| wikipedia 5 | 121,990 | 189,880,688 | 181.08 | 1,557 |
| wikipedia 6 | 243,981 | 478,842,959 | 456.66 | 1,963 |
| wikipedia 7 | 487,963 | 1,071,827,039 | 1,022.17 | 2,197 |
| wikipedia 8 | 975,926 | 2,315,093,668 | 2,207.85 | 2,372 |
| wikipedia 9 | 1,951,852 | 4,459,594,679 | 4,253.00 | 2,285 |
| wikipedia 10 | 3,903,703 | 8,933,518,792 | 8,519.67 | 2,288 |
| reads 1 | 100,000 | 9,030,390 | 8.61 | 90 |
| reads 2 | 200,000 | 17,703,050 | 16.88 | 89 |
| reads 3 | 400,000 | 36,808,318 | 35.10 | 92 |
| reads 4 | 800,000 | 75,089,460 | 71.61 | 94 |
| reads 5 | 1,600,000 | 149,953,139 | 143.01 | 94 |
| reads 6 | 3,200,000 | 302,041,259 | 288.05 | 94 |
| reads 7 | 6,400,000 | 604,318,315 | 576.32 | 94 |
| reads 8 | 12,800,000 | 1,209,578,418 | 1,153.54 | 94 |
| reads 9 | 25,600,000 | 2,419,646,287 | 2,307.55 | 95 |
| reads 10 | 32,621,862 | 3,082,739,100 | 2,939.93 | 94 |
| protein 1 | 100,000 | 26,198,280 | 24.98 | 262 |
| protein 2 | 200,000 | 52,503,813 | 50.07 | 263 |
| protein 3 | 400,000 | 106,286,416 | 101.36 | 266 |
| protein 4 | 800,000 | 219,589,476 | 209.42 | 274 |
| protein 5 | 1,600,000 | 531,194,430 | 506.59 | 332 |
| protein 6 | 3,200,000 | 1,253,483,804 | 1,195.42 | 392 |
| protein 7 | 6,400,000 | 2,667,015,568 | 2,543.46 | 417 |
| protein 8 | 12,800,000 | 5,162,366,462 | 4,923.22 | 403 |
| protein 9 | 25,600,000 | 9,070,832,678 | 8,650.62 | 354 |
| protein 10 | 50,825,784 | 16,931,428,229 | 16,147.07 | 333 |
Running time (seconds):
| Dataset | SAIS (int) | SACA-K (int) | SAIS | SACA-K | gSAIS | gSACA-K |
|---|---|---|---|---|---|---|
| pages 1 | 2.90E-01 | 4.10E-01 | 1.90E-01 | 1.20E-01 | 1.90E-01 | 1.20E-01 |
| pages 2 | 3.43E+00 | 3.35E+00 | 3.38E+00 | 2.09E+00 | 2.22E+00 | 2.06E+00 |
| pages 3 | 1.06E+01 | 1.01E+01 | 8.61E+00 | 7.60E+00 | 9.12E+00 | 7.65E+00 |
| pages 4 | 1.75E+01 | 1.59E+01 | 1.50E+01 | 1.25E+01 | 1.48E+01 | 1.23E+01 |
| pages 5 | 4.44E+01 | 3.89E+01 | 3.78E+01 | 3.21E+01 | 3.82E+01 | 3.17E+01 |
| pages 6 | 1.94E+02 | 1.57E+02 | 1.76E+02 | 1.35E+02 | 1.75E+02 | 1.33E+02 |
| pages 7 | 4.09E+02 | 3.26E+02 | 3.74E+02 | 2.79E+02 | 3.73E+02 | 2.76E+02 |
| pages 8 | 1.12E+03 | 8.88E+02 | 1.00E+03 | 9.22E+02 | 1.00E+03 | 7.31E+02 |
| pages 9 | 1.54E+03 | 1.33E+03 | 1.31E+03 | 1.02E+03 | 1.31E+03 | 9.89E+02 |
| pages 10 | 2.57E+03 | 2.17E+03 | 2.09E+03 | 1.61E+03 | 2.09E+03 | 1.56E+03 |
| revesion 1 | 1.20E-02 | 1.00E-02 | 9.00E-03 | 8.00E-03 | 8.00E-03 | 7.00E-03 |
| revesion 2 | 2.00E-02 | 1.50E-02 | 1.40E-02 | 1.20E-02 | 1.40E-02 | 1.20E-02 |
| revesion 3 | 6.60E-02 | 6.70E-02 | 5.60E-02 | 5.30E-02 | 5.70E-02 | 5.30E-02 |
| revesion 4 | 2.30E-01 | 2.40E-01 | 1.60E-01 | 1.50E-01 | 1.50E-01 | 1.50E-01 |
| revesion 5 | 6.30E-01 | 6.80E-01 | 3.80E-01 | 3.10E-01 | 3.40E-01 | 3.20E-01 |
| revesion 6 | 3.89E+00 | 4.32E+00 | 3.37E+00 | 3.07E+00 | 3.12E+00 | 2.92E+00 |
| revesion 7 | 1.04E+01 | 1.01E+01 | 8.83E+00 | 7.72E+00 | 9.52E+00 | 7.70E+00 |
| revesion 8 | 1.96E+01 | 1.83E+01 | 1.73E+01 | 1.48E+01 | 1.71E+01 | 1.47E+01 |
| revesion 9 | 5.56E+01 | 4.87E+01 | 4.98E+01 | 4.07E+01 | 4.89E+01 | 3.99E+01 |
| revesion 10 | 2.12E+02 | 1.70E+02 | 1.93E+02 | 1.45E+02 | 1.87E+02 | 1.39E+02 |
| influenza 1 | 8.40E-02 | 6.80E-02 | 6.60E-02 | 6.50E-02 | 6.70E-02 | 6.50E-02 |
| influenza 2 | 1.58E-01 | 1.61E-01 | 1.23E-01 | 1.24E-01 | 1.30E-01 | 1.24E-01 |
| influenza 3 | 4.23E-01 | 4.24E-01 | 2.68E-01 | 2.46E-01 | 2.69E-01 | 2.54E-01 |
| influenza 4 | 1.21E+00 | 1.17E+00 | 6.30E-01 | 6.20E-01 | 6.70E-01 | 6.10E-01 |
| influenza 5 | 2.96E+00 | 2.92E+00 | 1.67E+00 | 1.58E+00 | 1.75E+00 | 1.54E+00 |
| influenza 6 | 8.89E+00 | 8.70E+00 | 6.67E+00 | 6.16E+00 | 6.70E+00 | 6.08E+00 |
| influenza 7 | 2.19E+01 | 2.13E+01 | 1.84E+01 | 1.70E+01 | 1.85E+01 | 1.67E+01 |
| influenza 8 | 4.94E+01 | 4.57E+01 | 4.29E+01 | 3.81E+01 | 4.34E+01 | 3.76E+01 |
| influenza 9 | 1.10E+02 | 9.64E+01 | 9.66E+01 | 8.23E+01 | 9.85E+01 | 8.16E+01 |
| influenza 10 | 2.60E+02 | 2.12E+02 | 2.30E+02 | 1.82E+02 | 2.32E+02 | 1.80E+02 |
| wikipedia 1 | 3.41E+00 | 3.37E+00 | 1.98E+00 | 1.92E+00 | 2.41E+00 | 2.12E+00 |
| wikipedia 2 | 8.12E+00 | 7.77E+00 | 6.71E+00 | 6.25E+00 | 6.48E+00 | 5.99E+00 |
| wikipedia 3 | 1.95E+01 | 1.83E+01 | 1.78E+01 | 1.50E+01 | 1.65E+01 | 1.47E+01 |
| wikipedia 4 | 4.24E+01 | 3.79E+01 | 4.02E+01 | 3.23E+01 | 3.77E+01 | 3.15E+01 |
| wikipedia 5 | 9.05E+01 | 7.54E+01 | 8.52E+01 | 6.68E+01 | 8.33E+01 | 6.52E+01 |
| wikipedia 6 | 2.72E+02 | 2.03E+02 | 2.53E+02 | 1.83E+02 | 2.47E+02 | 1.81E+02 |
| wikipedia 7 | 6.86E+02 | 4.98E+02 | 6.15E+02 | 4.32E+02 | 6.24E+02 | 4.27E+02 |
| wikipedia 8 | 1.96E+03 | 1.43E+03 | 1.54E+03 | 1.09E+03 | 1.54E+03 | 1.06E+03 |
| wikipedia 9 | 4.40E+03 | 3.47E+03 | 3.25E+03 | 2.33E+03 | 3.62E+03 | 2.35E+03 |
| wikipedia 10 | 7.89E+03 | 6.18E+03 | 7.07E+03 | 5.25E+03 | 7.08E+03 | 5.08E+03 |
| reads 1 | 1.76E+00 | 1.79E+00 | 1.06E+00 | 1.08E+00 | 1.07E+00 | 1.05E+00 |
| reads 2 | 4.63E+00 | 4.52E+00 | 4.22E+00 | 4.04E+00 | 3.24E+00 | 3.02E+00 |
| reads 3 | 1.20E+01 | 1.12E+01 | 1.11E+01 | 9.84E+00 | 1.02E+01 | 9.16E+00 |
| reads 4 | 2.85E+01 | 2.46E+01 | 2.74E+01 | 2.16E+01 | 2.54E+01 | 2.13E+01 |
| reads 5 | 6.29E+01 | 5.10E+01 | 6.24E+01 | 4.81E+01 | 5.86E+01 | 4.61E+01 |
| reads 6 | 1.38E+02 | 1.07E+02 | 1.39E+02 | 1.03E+02 | 1.31E+02 | 9.74E+01 |
| reads 7 | 3.08E+02 | 2.22E+02 | 2.99E+02 | 2.18E+02 | 2.81E+02 | 2.48E+02 |
| reads 8 | 6.90E+02 | 4.88E+02 | 6.52E+02 | 4.55E+02 | 6.10E+02 | 4.19E+02 |
| reads 9 | 2.07E+03 | 1.83E+03 | 1.49E+03 | 1.03E+03 | 1.39E+03 | 9.36E+02 |
| reads 10 | 2.16E+03 | 1.68E+03 | 1.94E+03 | 1.37E+03 | 1.81E+03 | 1.24E+03 |
| protein 1 | 1.01E+01 | 9.32E+00 | 6.94E+00 | 6.15E+00 | 8.30E+00 | 7.30E+00 |
| protein 2 | 2.35E+01 | 2.08E+01 | 1.88E+01 | 1.62E+01 | 2.07E+01 | 1.74E+01 |
| protein 3 | 5.51E+01 | 4.56E+01 | 4.78E+01 | 3.89E+01 | 5.10E+01 | 3.98E+01 |
| protein 4 | 1.27E+02 | 9.93E+01 | 1.19E+02 | 9.03E+01 | 1.24E+02 | 9.01E+01 |
| protein 5 | 3.63E+02 | 2.55E+02 | 3.44E+02 | 2.39E+02 | 3.39E+02 | 2.34E+02 |
| protein 6 | 9.71E+02 | 6.63E+02 | 8.99E+02 | 5.85E+02 | 8.97E+02 | 5.73E+02 |
| protein 7 | 2.52E+03 | 1.88E+03 | 2.22E+03 | 1.47E+03 | 2.20E+03 | 1.41E+03 |
| protein 8 | 5.13E+03 | 3.88E+03 | 5.34E+03 | 3.51E+03 | 4.60E+03 | 3.04E+03 |
| protein 9 | 9.45E+03 | 7.17E+03 | 1.02E+04 | 7.34E+03 | 8.71E+03 | 5.96E+03 |
| protein 10 | 2.13E+04 | 1.65E+04 | 1.87E+04 | 1.26E+04 | 1.86E+04 | 1.22E+04 |
Space (MiB):
| Dataset | SAIS (int) | SACA-K (int) | SAIS | SACA-K | gSAIS | gSACA-K |
|---|---|---|---|---|---|---|
| pages 1 | 18.50 | 18.09 | 11.72 | 11.31 | 11.72 | 11.31 |
| pages 2 | 114.76 | 112.21 | 72.68 | 70.13 | 72.68 | 70.13 |
| pages 3 | 273.43 | 267.36 | 173.17 | 167.10 | 173.17 | 167.10 |
| pages 4 | 412.69 | 403.52 | 261.37 | 252.20 | 261.37 | 252.20 |
| pages 5 | 932.11 | 911.46 | 590.32 | 569.66 | 590.32 | 569.66 |
| pages 6 | 3,215.52 | 3,144.44 | 2,036.36 | 1,965.28 | 2,036.36 | 1,965.28 |
| pages 7 | 6,560.70 | 6,415.45 | 4,154.91 | 4,009.66 | 4,154.91 | 4,009.66 |
| pages 8 | 16,597.26 | 16,230.27 | 10,510.91 | 10,143.92 | 10,510.91 | 10,143.92 |
| pages 9 | 40,680.40 | 40,220.86 | 23,083.78 | 22,624.23 | 23,083.78 | 22,624.23 |
| pages 10 | 62,034.13 | 61,334.01 | 35,200.50 | 34,500.38 | 35,200.50 | 34,500.38 |
| revesion 1 | 0.78 | 0.76 | 0.49 | 0.47 | 0.49 | 0.47 |
| revesion 2 | 2.03 | 1.99 | 1.29 | 1.24 | 1.29 | 1.24 |
| revesion 3 | 7.14 | 6.98 | 4.52 | 4.36 | 4.52 | 4.36 |
| revesion 4 | 16.33 | 15.96 | 10.34 | 9.98 | 10.34 | 9.98 |
| revesion 5 | 33.52 | 32.77 | 21.23 | 20.48 | 21.24 | 20.48 |
| revesion 6 | 125.30 | 122.53 | 79.36 | 76.58 | 79.36 | 76.58 |
| revesion 7 | 266.61 | 260.70 | 168.85 | 162.93 | 168.85 | 162.93 |
| revesion 8 | 467.31 | 456.94 | 295.96 | 285.57 | 295.96 | 285.57 |
| revesion 9 | 1,125.41 | 1,100.52 | 712.73 | 687.80 | 712.73 | 687.80 |
| revesion 10 | 3,272.45 | 3,200.13 | 2,072.43 | 2,000.03 | 2,072.43 | 2,000.03 |
| influenza 1 | 7.30 | 7.06 | 4.65 | 4.41 | 4.65 | 4.41 |
| influenza 2 | 13.97 | 13.54 | 8.88 | 8.46 | 8.89 | 8.46 |
| influenza 3 | 28.27 | 27.48 | 17.95 | 17.17 | 17.97 | 17.17 |
| influenza 4 | 55.30 | 53.86 | 35.08 | 33.65 | 35.11 | 33.65 |
| influenza 5 | 110.36 | 107.63 | 69.96 | 67.24 | 70.01 | 67.24 |
| influenza 6 | 257.69 | 251.55 | 163.27 | 157.16 | 163.39 | 157.16 |
| influenza 7 | 553.21 | 540.36 | 350.40 | 337.61 | 350.64 | 337.61 |
| influenza 8 | 1,116.44 | 1,090.85 | 707.00 | 681.55 | 707.51 | 681.55 |
| influenza 9 | 2,261.16 | 2,209.91 | 1,431.85 | 1,380.72 | 1,432.73 | 1,380.72 |
| influenza 10 | 4,665.13 | 4,559.85 | 2,953.86 | 2,848.97 | 2,955.75 | 2,848.97 |
| wikipedia 1 | 107.45 | 101.53 | 69.39 | 63.44 | 69.39 | 63.44 |
| wikipedia 2 | 207.41 | 196.42 | 133.77 | 122.73 | 133.78 | 122.73 |
| wikipedia 3 | 426.01 | 404.49 | 274.35 | 252.74 | 274.37 | 252.74 |
| wikipedia 4 | 810.54 | 771.36 | 521.34 | 481.96 | 521.36 | 481.96 |
| wikipedia 5 | 1,519.14 | 1,449.14 | 975.82 | 905.42 | 975.88 | 905.42 |
| wikipedia 6 | 3,820.79 | 3,654.21 | 2,450.67 | 2,283.30 | 2,450.81 | 2,283.30 |
| wikipedia 7 | 8,530.61 | 8,179.25 | 5,463.79 | 5,110.87 | 5,464.09 | 5,110.87 |
| wikipedia 8 | 36,372.60 | 35,332.97 | 20,916.24 | 19,870.61 | 20,917.68 | 19,870.61 |
| wikipedia 9 | 69,951.59 | 68,062.91 | 40,180.41 | 38,277.01 | 40,180.59 | 38,277.01 |
| wikipedia 10 | 140,078.79 | 136,344.46 | 80,440.72 | 76,677.01 | 80,441.12 | 76,677.01 |
| reads 1 | 72.91 | 69.28 | 47.04 | 43.06 | 47.07 | 43.06 |
| reads 2 | 142.65 | 135.83 | 91.90 | 84.42 | 92.00 | 84.42 |
| reads 3 | 295.69 | 282.35 | 175.52 | 175.52 | 190.38 | 175.52 |
| reads 4 | 600.92 | 575.94 | 385.35 | 358.06 | 386.09 | 358.06 |
| reads 5 | 1,194.90 | 1,150.16 | 763.98 | 715.03 | 765.88 | 715.03 |
| reads 6 | 2,396.03 | 2,316.60 | 1,527.06 | 1,440.25 | 1,531.88 | 1,440.25 |
| reads 7 | 4,777.69 | 4,635.00 | 3,036.75 | 2,881.62 | 3,048.72 | 2,881.62 |
| reads 8 | 9,543.64 | 9,277.18 | 6,065.95 | 5,767.72 | 6,083.01 | 5,767.72 |
| reads 9 | 37,781.02 | 37,116.19 | 21,555.19 | 20,767.99 | 21,628.14 | 20,767.99 |
| reads 10 | 48,114.93 | 47,287.75 | 27,450.08 | 26,459.36 | 27,535.43 | 26,459.36 |
| protein 1 | 212.12 | 200.26 | 137.01 | 124.92 | 137.16 | 124.92 |
| protein 2 | 424.63 | 401.34 | 274.11 | 250.36 | 274.41 | 250.36 |
| protein 3 | 857.04 | 812.43 | 552.33 | 506.81 | 552.95 | 506.81 |
| protein 4 | 1,768.69 | 1,678.39 | 1,139.24 | 1,047.09 | 1,140.44 | 1,047.09 |
| protein 5 | 4,288.93 | 4,058.80 | 2,767.10 | 2,532.93 | 2,769.17 | 2,532.93 |
| protein 6 | 10,081.31 | 9,575.53 | 6,490.38 | 5,977.08 | 6,495.06 | 5,977.08 |
| protein 7 | 42,240.02 | 40,744.26 | 24,411.26 | 22,891.18 | 24,435.77 | 22,891.18 |
| protein 8 | 81,798.41 | 78,869.12 | 47,289.48 | 44,308.95 | 47,335.89 | 44,308.95 |
| protein 9 | 143,689.08 | 138,605.24 | 83,036.60 | 77,855.58 | 83,134.74 | 77,855.58 |
| protein 10 | 267,478.92 | 258,740.86 | 154,213.88 | 145,323.62 | 154,449.44 | 145,323.62 |
Workspace (MiB, but SACA-K and gSACA-K):
| Dataset | SAIS (int) | SACA-K (int) | SAIS | SACA-K | gSAIS | gSACA-K |
|---|---|---|---|---|---|---|
| pages 1 | 0.41 | 0.00 | 0.41 | 1,024 | 0.41 | 1,024 |
| pages 2 | 2.55 | 0.00 | 2.55 | 1,024 | 2.55 | 1,024 |
| pages 3 | 6.07 | 0.00 | 6.07 | 1,024 | 6.07 | 1,024 |
| pages 4 | 9.17 | 0.00 | 9.17 | 1,024 | 9.17 | 1,024 |
| pages 5 | 20.66 | 0.00 | 20.66 | 1,024 | 20.66 | 1,024 |
| pages 6 | 71.08 | 0.00 | 71.08 | 1,024 | 71.08 | 1,024 |
| pages 7 | 145.25 | 0.00 | 145.25 | 1,024 | 145.25 | 1,024 |
| pages 8 | 367.00 | 0.00 | 367.00 | 1,024 | 367.00 | 1,024 |
| pages 9 | 459.55 | 0.01 | 459.55 | 1,024 | 459.55 | 1,024 |
| pages 10 | 700.13 | 0.01 | 700.13 | 1,024 | 700.13 | 1,024 |
| revesion 1 | 0.02 | 0.00 | 0.02 | 1,024 | 0.02 | 1,024 |
| revesion 2 | 0.05 | 0.00 | 0.05 | 1,024 | 0.05 | 1,024 |
| revesion 3 | 0.16 | 0.00 | 0.16 | 1,024 | 0.16 | 1,024 |
| revesion 4 | 0.37 | 0.00 | 0.37 | 1,024 | 0.37 | 1,024 |
| revesion 5 | 0.76 | 0.00 | 0.76 | 1,024 | 0.76 | 1,024 |
| revesion 6 | 2.78 | 0.01 | 2.78 | 1,024 | 2.78 | 1,024 |
| revesion 7 | 5.92 | 0.01 | 5.92 | 1,024 | 5.92 | 1,024 |
| revesion 8 | 10.39 | 0.02 | 10.39 | 1,024 | 10.39 | 1,024 |
| revesion 9 | 24.93 | 0.04 | 24.93 | 1,024 | 24.93 | 1,024 |
| revesion 10 | 72.40 | 0.08 | 72.40 | 1,024 | 72.40 | 1,024 |
| influenza 1 | 0.25 | 0.00 | 0.24 | 1,024 | 0.25 | 1,024 |
| influenza 2 | 0.43 | 0.01 | 0.43 | 1,024 | 0.43 | 1,024 |
| influenza 3 | 0.80 | 0.01 | 0.78 | 1,024 | 0.80 | 1,024 |
| influenza 4 | 1.46 | 0.02 | 1.43 | 1,024 | 1.46 | 1,024 |
| influenza 5 | 2.78 | 0.05 | 2.72 | 1,024 | 2.78 | 1,024 |
| influenza 6 | 6.23 | 0.09 | 6.11 | 1,024 | 6.23 | 1,024 |
| influenza 7 | 13.04 | 0.19 | 12.80 | 1,024 | 13.04 | 1,024 |
| influenza 8 | 25.96 | 0.38 | 25.46 | 1,024 | 25.96 | 1,024 |
| influenza 9 | 52.00 | 0.75 | 51.13 | 1,024 | 52.00 | 1,024 |
| influenza 10 | 106.78 | 1.50 | 104.89 | 1,024 | 106.78 | 1,024 |
| wikipedia 1 | 5.96 | 0.03 | 5.96 | 1,024 | 5.96 | 1,024 |
| wikipedia 2 | 11.05 | 0.06 | 11.04 | 1,024 | 11.05 | 1,024 |
| wikipedia 3 | 21.63 | 0.12 | 21.62 | 1,024 | 21.63 | 1,024 |
| wikipedia 4 | 39.41 | 0.23 | 39.38 | 1,024 | 39.41 | 1,024 |
| wikipedia 5 | 70.46 | 0.47 | 70.40 | 1,024 | 70.46 | 1,024 |
| wikipedia 6 | 167.51 | 0.93 | 167.37 | 1,024 | 167.51 | 1,024 |
| wikipedia 7 | 353.22 | 1.86 | 352.92 | 1,024 | 353.22 | 1,024 |
| wikipedia 8 | 1,047.08 | 7.45 | 1,045.63 | 1,024 | 1,047.08 | 1,024 |
| wikipedia 9 | 1,903.58 | 14.89 | 1,903.40 | 1,024 | 1,903.58 | 1,024 |
| wikipedia 10 | 3,764.11 | 29.78 | 3,763.71 | 1,024 | 3,764.11 | 1,024 |
| reads 1 | 4.01 | 0.38 | 3.98 | 1,024 | 4.01 | 1,024 |
| reads 2 | 7.58 | 0.76 | 7.48 | 1,024 | 7.58 | 1,024 |
| reads 3 | 14.86 | 1.53 | 14.58 | 1,024 | 14.86 | 1,024 |
| reads 4 | 28.04 | 3.05 | 27.30 | 1,024 | 28.04 | 1,024 |
| reads 5 | 50.85 | 6.10 | 48.94 | 1,024 | 50.85 | 1,024 |
| reads 6 | 91.63 | 12.21 | 86.82 | 1,024 | 91.63 | 1,024 |
| reads 7 | 167.11 | 24.42 | 155.14 | 1,024 | 167.11 | 1,024 |
| reads 8 | 315.29 | 48.83 | 298.24 | 1,024 | 315.29 | 1,024 |
| reads 9 | 860.14 | 195.31 | 787.20 | 1,024 | 860.14 | 1,024 |
| reads 10 | 1,076.07 | 248.89 | 990.72 | 1,024 | 1,076.07 | 1,024 |
| protein 1 | 12.24 | 0.38 | 12.09 | 1,024 | 12.24 | 1,024 |
| protein 2 | 24.06 | 0.76 | 23.75 | 1,024 | 24.06 | 1,024 |
| protein 3 | 46.14 | 1.53 | 45.52 | 1,024 | 46.14 | 1,024 |
| protein 4 | 93.36 | 3.05 | 92.16 | 1,024 | 93.36 | 1,024 |
| protein 5 | 236.24 | 6.10 | 234.17 | 1,024 | 236.24 | 1,024 |
| protein 6 | 517.99 | 12.21 | 513.30 | 1,024 | 517.99 | 1,024 |
| protein 7 | 1,544.59 | 48.83 | 1,520.08 | 1,024 | 1,544.59 | 1,024 |
| protein 8 | 3,026.95 | 97.66 | 2,980.53 | 1,024 | 3,026.95 | 1,024 |
| protein 9 | 5,279.16 | 195.31 | 5,181.02 | 1,024 | 5,279.16 | 1,024 |
| protein 10 | 9,125.83 | 387.77 | 8,890.27 | 1,024 | 9,125.83 | 1,024 |
##references
[1] G. Nong, S. Zhang, and W. H. Chan, “Two efficient algorithms for linear time suffix array construction,” IEEE Trans. Comput., vol. 60, no. 10, pp. 1471–1484, 2011
[2] Nong, G. Practical linear-time O(1)-workspace suffix sorting for constant alphabets,” ACM Trans. Inform. Syst., vol. 31, no. 3, pp. 1–15, 2013