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Table 3 Grammar performance.

From: Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

  

Sensitivity % (PPV %)

Grammar

Full Benchmarking

Set Sensitivity % (PPV %)

RNase P

SRP

tmRNA

G1

17 (12)

14 (11)

37 (32)

10(6)

G3

34 (31)

37 (35)

28 (28)

31 (22)

G4

10 (8)

10(8)

19 (17)

4(2)

G5

3(4)

3(4)

2(3)

4(3)

G6

47 (45)

49 (49)

47 (49)

44 (33)

G2

36 (25)

31 (23)

59 (48)

33 (17)

G7

45 (43)

46 (46)

50 (52)

40 (30)

G8

46 (44)

46 (46)

52 (53)

44 (32)

G6S

49 (45)

50 (50)

50 (51)

44 (32)

mfold v3.1.2

56 (48)

56 (51)

70 (66)

46 (30)

Vienna RNA

55 (47)

55 (51)

67 (64)

45 (30)

PKNOTS

50 (41)

53 (46)

58 (55)

38 (24)

RNAstructure

56 (47)

58 (52)

62 (58)

46 (30)

Pfold

39 (69)

42 (76)

35 (64)

33 (54)

  1. The first section contains simple grammars, the second contains stacking grammars, and the last section contains other available software packages that predict secondary structure. The nine grammars were trained on rRNA as described in the text. The second column gives the performance on the full benchmarking dataset, which is subdivided into each family in the subsequent columns. The metrics are calculated over base pairs as described in the text, evaluating the metrics over individual sequences shows similar results (data not shown).