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Table 5 Running time and speedup for the DNA data

From: RefSelect: a reference sequence selection algorithm for planted (l, d) motif search

(l, d)   qPMS7 TravStrR PMS8
T 1 T rs  + T 2 speedup T 1 T rs  + T 2 speedup T 1 T rs  + T 2 speedup
(15, 5) min 149.00s 128.00s 1.10 68.34 s 64.46 s 1.03 38.51 s 37.73 s 1.04
ave 173.00s 157.67 s 73.84 s 71.61 s 65.43 s 63.21 s
max 220.00s 196.00s 91.96 s 85.52 s 113.16 s 106.54 s
(17, 6) min 557.00s 504.00s 1.08 230.41 s 185.54 s 1.03 244.95 s 216.00s 1.04
ave 660.40s 611.80s 263.39 s 255.38 s 387.80s 371.42 s
max 884.00s 756.00s 322.78 s 319.74 s 601.29 s 601.20s
(19, 7) min 2520.00s 2357.00s 1.06 1009.06 s 970.67 s 1.05 1105.88 s 1092.14 s 1.04
ave 2911.00s 2737.20s 1116.18 s 1060.56 s 1834.32 s 1753.06 s
max 3846.00s 3553.00s 1281.81 s 1264.79 s 3064.09 s 2811.09 s
(21, 8) min 12144.00s 11343.00s 1.03 3403.84 s 3168.97 s 1.00 7997.65 7896.77 s 1.13
ave 12791.40s 12444.00s 4377.85 s 4357.19 s 12494.79 s 11102.56 s
max 13701.00s 14029.00s 5306.58 s 5301.84 s 14243.2 s 11395.31 s
(23, 9) min 61512.00s 61561.00s 1.07 14456.36 s 14184.14 s 1.00 23984.70s 22081.70s 1.11
ave 68741.60s 64022.60s 18234.85 s 18157.41 s 38705.98 s 34847.10s
max 77427.00s 68709.00s 21315.48 s 22094.73 s 61160.00s 61278.10s
  1. s: seconds; −o:over 48 hours; T 1 and T 2: running time of a PMS algorithm on the input sequences of original order and new order; T rs : running time of RefSelect; min, average and max: the minimum, average and maximum running time on five data sets; speedup: average T 1/average T rs  + T 2.