Table 1

TPR values at 1% FPR (TPR01) for Hierarchical Cluster Methods and Tree Cutting Strategies.

Group#

Tree Cutting Strategy

Hierarchical Cluster Method

VAST Nres

VAST Pcli

SHEBA Nres

SHEBA Zscore

DALI Nres

DALI Zscore

Average

Range


2

Level

Average

28

24

23

33

28

38

29

15

2

Level

Complete

28

31

29

40

39

27

32

13

2

Level

Single

14

10

12

21

16

8

13

13

2

Level

Ward

50

48

48

54

50

49

50

6

3

Largest Size

Average

54

50

48

59

55

41

51

18

3

Largest Size

Complete

44

44

43

43

50

51

46

8

3

Largest Size

Single

29

22

27

39

34

13

27

26

3

Largest Size

Ward

61

59

61

58

62

65

61

7

3

Tree Completeness

Ward

57

59

61

56

56

63

58

7

3

Highest tree

Ward

57

61

62

56

57

63

59

7

1

Tree skewness

Ward

25

15

26

22

31

21

23

10

1

Longest branch

Ward

29

20

26

22

27

13

23

16

2

Maximum Entropy

Ward

45

40

43

46

58

48

46

18

1

BestTPR

Ward

12

13

13

10

8

16

12

8

4

Best ratio TPR &FPR

Ward

73

72

73

71

75

75

73

4

4

MI

Ward

73

71

72

71

76

76

73

5

Direct pw§

none

50

52

60

61

52

67

57

17


§Direct pw is the direct pairwise comparison between pairwise similarity scores and SCOP folds in the C class, and does not involve clustering.

# the group to which the strategy belongs.

Sam et al. BMC Bioinformatics 2008 9:74   doi:10.1186/1471-2105-9-74

Open Data