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Table 4 Running time and speedup for the protein 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, 7) min 93.00s 85.00s 6.58 5.80s 5.63 s 1.00 2.21 s 3.64 s 1.89
ave 722.40s 109.80s 7.51 s 7.49 s 288.33 s 178.43 s
max 2596.00s 122.00s 8.89 s 8.74 s 1126.80s 544.00s
(17, 8) min 131.00s 120.00s 7.68 11.88 s 8.98 s 4.03 390.13 s 8.52 s 5.85
ave 1204.40s 156.80s 76.98 s 19.10s 1647.89 s 281.83 s
max 3742.00s 214.00s 207.32 s 54.01 s 3092.82 s 719.78 s
(19, 9) min 820.00s 140.00s 86.22 11.58 s 11.25 s 76.38 189.07 s 17.11 s 2.21
ave 18502.20s 214.60s 1591.67 s 20.84 s 14619.67 s 6629.83 s
max 37121.00s 287.00s 4355.44 s 30.23 s 53376.12 s 17235.40s
(21, 10) min 191.00s 161.00s >118.94 22.47 s 22.28 s 61.63 18268.00s 3022.00s >9.65
ave -o 671.40s 1745.09 s 24.25 s -o 17905.40s
max -o 1783.00s 6453.27 s 53.06 s -o 31054.00s
(23, 11) min 53978.00s 242.00s >34.77 44.30s 12.19 s 15.56 6327.12 s 1608.23 s >12.89
ave -o 4970.00s 3033.99 s 195.04 s -o 13409.80s
max -o 17141.00s 10909.72 s 378.31 s -o 50421.00s
  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, ave and max: the minimum, average and maximum running time on five data sets; speedup: average T 1/average T rs  + T 2.