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Table 4 Execution time of the different approaches on the 14 sample queries in seconds

From: START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries

Query

Number of input tracks

Number of input intervals

Number of output intervals

START

Bedtools

Python

Galaxy

SQ1

1

57,059,743

23,857,046

207

407

1171

N/A

SQ2

2

11,517,945

33,312

50

135

184

N/A

SQ3

2

51,417

14,026

39

0.04

0.3

23

SQ4

2

11,517,945

1,054,854

47

21

42

408

SQ5

1

8,898,501

450,380

52

7

125

270

SQ6

2

18,839

5702

46

0.04

21

N/A

SQ7

1

2,619,444

36,366

31

6

5

44

SQ8

1

2,619,444

1

33

2

3

30

CQ1

52

1,514,863

2,590,502

86

N/A

36

N/A

CQ2

3

2,938,174

29,225

300

N/A

7

N/A

CQ3

53

4,134,307

76,041

1340

N/A

84

N/A

CQ4

100

32,297,907

68,031

1680

262

420

N/A

CQ5

5

257,369,824

264

360

N/A

5289

N/A

CQ6

2

65,412,859

4,006,220

119

207

483

N/A

  1. N/A indicates cases in which we were unable to find a trivial way to perform the analysis using the approach