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Table 2 BRaliBase accuracy

From: Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars

Sequence

Program

Ref. basepairs

Pred. basepairs

Sensitivity, %

Selectivity, %

Correlation, %

tRNA (M)

PPfold

20

21

100.0

100.0

100.0

tRNA (M)

pfold

20

21

100.0

100.0

100.0

tRNA (H)

PPfold

20

21

100.0

100.0

100.0

tRNA (H)

pfold

20

21

100.0

100.0

100.0

RNaseP (M)

PPfold

110

110

86.4

96.0

91.2

RNaseP (M)

pfold

110

110

86.4

96.0

91.2

RNaseP (H)

PPfold

110

69

43.6

71.6

57.6

RNaseP (H)

pfold

110

69

43.6

71.6

57.6

SSU (M)

PPfold

468

420

74.4

86.1

80.2

SSU (M)

pfold

468

0

0.0

0.0

0.0

SSU (H)

PPfold

468

373

68.4

89.1

78.8

SSU (H)

pfold

468

373

68.4

89.1

78.8

LSU (M)

PPfold

839

830

58.2

62.5

60.3

LSU (M)

pfold

839

0

0.0

0.0

0.0

LSU (H)

PPfold

839

754

52.2

61.0

56.6

LSU (H)

pfold

839

0

0.0

0.0

0.0

  1. The results of our tests on the BRaliBase I dataset, using the comparison script available at http://projects.binf.ku.dk/pgardner/bralibase/bralibase1.html, are shown, both for pfold and PPfold. We carried out stem-extension separately on the PPfold predictions, as it is not implemented in PPfold at present. M: medium-similarity, H: high-similarity