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Table 3 Number of true positives (nTPs), false negatives (nFNs), and false positives (nFPs) detected by different TFBS prediction tools

From: The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes

Tool

Overlap percentage*

80%

90%

100%

nTPs

nFNs

nFPs

nTPs

nFNs

nFPs

nTPs

nFNs

nFPs

Ciiider

43

17

10

43

17

10

34

26

9

DWT-toolbox

60

0

65

60

0

65

45

15

65

FIMO

57

3

17

57

3

17

45

15

17

HOMER

58

2

1002

58

2

1002

43

17

1002

INSECT 2.0

45

15

12

45

15

12

36

24

12

Matrix scan

50

10

13

50

10

13

41

19

13

MCAST

51

9

0

51

9

0

42

18

0

MOODS

52

8

12

52

8

12

43

17

12

Morpheus

54

6

142

51

9

142

46

14

142

MotEvo

60

0

35

60

0

35

45

15

35

PWMScan

57

3

20

57

3

20

45

15

20

TFBStools

9

51

2

0

60

2

0

60

2

  1. * Overlap percentage: the percentage overlap between the length of predicted and known binding sites
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BMC Bioinformatics

ISSN: 1471-2105

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