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Table 7 Results of spd qPMS algorithms on the first group of simulated datasets

From: SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets

(l, d)

conservation

T s

qPMS9

TravStrR

T D

T D

Speedup

T D

T D

Speedup

(9, 2)

high

33.0 s

N

2.3 s

> 4895

N

0.3 s

> 5189

intermediate

17.0 s

N

1.8 s

> 9191

N

0.2 s

> 10,047

low

12.8 s

N

1.7 s

> 11,917

24.2 h

0.1 s

6766

(11, 3)

high

26.8 s

N

3.5 s

> 5703

N

0.6 s

> 6307

intermediate

18.0 s

N

3.1 s

> 8190

N

0.3 s

> 9443

low

13.0 s

N

3.0 s

> 10,800

N

0.3 s

> 12,992

(13, 4)

high

28.8 s

N

8.4 s

> 46,456

N

2.8 s

> 5468

intermediate

20.2 s

N

7.6 s

> 6216

N

1.9 s

> 7819

low

13.0 s

N

7.0 s

> 8640

N

1.4 s

> 12,000

(15, 5)

high

29.4 s

N

25.3 s

> 3159

N

29.5 s

> 2934

intermediate

20.2 s

N

13.6 s

> 5112

N

10.6 s

> 5610

low

13.0 s

N

12.5 s

> 6776

N

5.6 s

> 9290

(17, 6)

high

29.4 s

N

9.1 m

> 300

N

6.4 m

> 415

intermediate

19.8 s

N

47.8 s

> 2556

N

36.8 s

> 3053

low

13.0 s

N

16.1 s

> 5938

N

14.0 s

> 6400

(19, 7)

high

32.0 s

N

N

N

N

1.1 h

> 43

intermediate

21.0 s

N

5.0 m

> 541

N

4.5 m

> 598

low

12.8 s

N

30.7 s

> 3972

N

42.1 s

> 3148

  1. s seconds, m minutes, h hours, N no result because the running time exceeds 48 h; T s : running time of SamSelect; T D and T D ’: running time of a qPMS algorithm on the original dataset D and the sample sequence sets D’, respectively; speedup: T D / T s  + T D