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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.