Table 5

RNase P is a difficult data-set to study. Five sequences in the high similarity data-set are truncated at both the 5 and 3 prime ends (due to the primers used for sequencing these). Sequences in the medium similarity data-set are full-length but do not align well using traditional tools such as ClustalW. Values corresponding to the re-evaluation of ILM with pseudo-knot inclusive reference structures are indicated by "ILM-pknot".

E. coli RNase P: Comparative Methods


Algorithm

number of bps in reference

number of bps in prediction

True Positives (% sensitivity)

False Positives (% selectivity)

Correlation (%)


RNAalifold (H)

71

113

56 (78.9)

16 (77.8)

0.782 (78.3)

RNAalifold (H) + RNAfold-C

71

119

55 (77.5)

16 (77.5)

0.773 (77.5)

RNAalifold (M)

54

66

31 (57.4)

23 (57.4)

0.571 (57.4)

RNAalifold (M) + RNAfold-C

54

77

33 (61.1)

16 (67.3)

0.639 (64.2)

Pfold (H)

71

67

47 (66.2)

6 (88.7)

0.765 (77.4)

Pfold (M)

54

87

47 (87.0)

4 (92.2)

0.895 (89.6)

ILM (H)

71

124

31 (43.7)

54 (36.5)

0.395 (40.1)

ILM (M)

54

133

38 (70.4)

31 (55.1)

0.620 (62.7)

ILM-pknot (H)

110

124

53 (48.2)

65 (44.9)

0.463 (46.5)

ILM-pknot (M)

110

133

44 (40.0)

75 (37.0)

0.382 (38.5)

Plan B: Unaligned sequences

Carnac (H)

71

40

36 (50.7)

0 (100.0)

0.712 (75.4)

Carnac (H) + RNAfold-C

71

116

50 (70.4)

25 (66.7)

0.684 (68.5)

Carnac (M)

97

80

63 (64.9)

3 (95.5)

0.787 (80.2)

Carnac (M) + RNAfold-C

97

118

78 (80.4)

25 (75.7)

0.779 (78.1)

Foldalign (H)

71

41

14 (19.7)

25 (35.9)

0.265 (27.8)

Foldalign (M)

97

24

5 (5.2)

17 (22.7)

0.107 (13.9)

Dynalign (H)

71

95.13

28.63 (40.31)

41.50 (39.59)

0.3974 (39.96)

Dynalign (M)

97

103.20

31.00 (31.95)

61.50 (32.80)

0.3208 (32.39)

Plan C: Structure alignment

MARNA (H)

71

89

37 (52.1)

23 (61.7)

0.566 (56.9)

MARNA (M)

97

60

48 (49.5)

9 (84.2)

0.645 (66.8)

MARNA-trim (H)

71

52

37 (52.1)

3 (92.5)

0.694 (72.3)

MARNA-trim (M)

97

43

39 (40.2)

1 (97.5)

0.625 (68.9)

RNAforester (H)

71

114

40 (56.3)

31 (56.3)

0.562 (56.3)

RNAforester (M)

97

117

64 (66.0)

44 (59.3)

0.624 (62.6)


Gardner and Giegerich BMC Bioinformatics 2004 5:140   doi:10.1186/1471-2105-5-140

Open Data