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Table 4 Sensitivities of the Dynalign/LIBSVM classifier, RNAz, and QRNA broken down by percent identity.

From: Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

  

% sensitivity

% specificity

% identity range

N

% of real set

Dynalign (P > 0.819)

RNAz (P > 0.789)

QRNA

N

% of negative set

Dynalign (P <= 0.819)

RNAz (P <= 0.789)

QRNA

[0

10)

0

0

N/A

N/A

N/A

0

0

N/A

N/A

N/A

[10

20)

0

0

N/A

N/A

N/A

0

0

N/A

N/A

N/A

[20

30)

3

0.0033

100.0

0.0

66.6667

49

0.0271

97.9592

100.0

95.9184

[30

40)

1337

1.4767

71.4286

34.6298

48.6163

9037

4.9907

99.1922

97.0233

97.8975

[40

50)

22328

24.6612

63.6465

63.1539

46.5559

85008

46.9455

99.3612

98.8542

99.2789

[50

60)

42733

47.1984

73.0606

75.6488

56.2469

55602

30.7061

99.2320

99.5018

99.0306

[60

70)

17346

19.1586

88.4930

92.2461

86.0775

23952

13.2274

99.1566

99.3028

98.8143

[70

80)

4061

4.4854

94.5826

94.5087

94.1394

4672

2.5801

97.5813

98.4375

97.9238

[80

90)

2035

2.2477

95.5774

91.9410

93.9066

2062

1.1387

90.8341

98.1086

96.6052

[90

100)

654

0.7223

98.4709

72.6300

59.7859

654

0.3612

60.5505

96.7890

95.2599

[100 ]

42

0.0464

92.8571

61.9048

11.9048

42

0.0232

61.9048

90.4762

95.2381

totals

90539

100.0

75.3366

81.2854

62.0108

181078

100.0

98.9938

98.9927

98.9905

  1. A comparison of sensitivities of the three ncRNA classification/detection programs within each percent identity range. N is the number of sequences within each range. Probability cutoffs for RNAz and the Dynalign/LIBSVM classifier were selected such that overall specificities for the entire test set match the specificity of QRNA as closely as possible.
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BMC Bioinformatics

ISSN: 1471-2105

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