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Table 1 Results of RaligNAtor and blastn database searches for members of RNA families of different degrees of sequence identity in RFAM10.1

From: Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

     

RaligNAtor

  

RaligNAtor (sequence only)

blastn

Family Acc.

Size

Seq. ident.

K=d

#TP

#FP

AUC

(pAUC)

K=d

#TP

#FP

AUC

(pAUC)

#TP

#FP

AUC

(pAUC)

RF00032

9,900

48%

3

9,900

1,088,131

0.95

(0.17)

3

9,900

2,723,135

0.82

(0.09)

3,000

68

0.29

(0.05)

RF00080

688

52%

33

688

698,942

0.71

(0.08)

19

688

1,279,375

0.60

(0.06)

326

540

0.42

(0.06)

RF02003

176

52%

21

176

1,174,167

0.53

(0.03)

6

176

1,168,093

0.32

(0.00)

28

814

0.11

(0.01)

RF00458

16

53%

20

16

88

0.94

(0.18)

14

16

2,688

0.96

(0.18)

12

1,224

0.73

(0.13)

RF00685

131

55%

18

131

40,952

0.98

(0.19)

7

131

103,276

0.97

(0.19)

88

2,945

0.63

(0.10)

RF00167

1,244

56%

25

1,244

2,514,701

0.58

(0.04)

17

1,244

2,611,256

0.28

(0.00)

660

624

0.52

(0.10)

RF01705

598

56%

26

598

2,704,796

0.49

(0.02)

17

598

2,698,712

0.42

(0.00)

57

60

0.08

(0.01)

RF01852

1,050

56%

22

1,050

1,026,233

0.99

(0.19)

14

1,050

1,488,254

0.94

(0.17)

543

83,268

0.44

(0.06)

RF01734

584

57%

10

584

2,614,228

0.69

(0.05)

5

584

2,668,392

0.46

(0.01)

201

114

0.30

(0.05)

RF00556

201

58%

8

201

69,808

0.97

(0.18)

6

201

1,514,311

0.92

(0.15)

91

1,024

0.44

(0.08)

RF00713

14

58%

27

14

10,349

0.99

(0.19)

18

14

16,477

0.88

(0.16)

13

552

0.92

(0.18)

RF00170

41

59%

13

41

53

0.97

(0.18)

9

41

9,197

0.96

(0.18)

29

176

0.70

(0.14)

RF00706

69

59%

13

69

1

1.00

(0.20)

9

69

12

0.97

(0.19)

66

194

0.95

(0.18)

RF00747

29

59%

20

29

130

0.97

(0.18)

16

29

159,898

0.96

(0.18)

28

236

0.96

(0.19)

RF00778

20

59%

33

20

394,560

0.93

(0.17)

23

20

167,029

0.79

(0.13)

17

390

0.84

(0.16)

RF01065

118

59%

17

118

0

1.00

(0.20)

9

118

0

1.00

(0.20)

70

305

0.59

(0.11)

RF01733

9

63%

9

9

0

1.00

(0.20)

7

9

0

1.00

(0.20)

7

918

0.77

(0.15)

RF00522

415

67%

5

415

1,461

0.99

(0.19)

5

415

32,224

0.99

(0.19)

359

391

0.63

(0.10)

RF01862

15

67%

7

15

0

1.00

(0.20)

5

15

0

1.00

(0.20)

10

82

0.66

(0.13)

RF00104

406

69%

24

406

989,362

0.99

(0.19)

14

406

1,560,674

0.99

(0.19)

237

72

0.45

(0.07)

RF00165

431

69%

9

431

0

1.00

(0.20)

8

431

1

0.99

(0.19)

318

192

0.73

(0.14)

RF01185

108

69%

13

108

24,759

0.99

(0.19)

13

108

24,759

0.99

(0.19)

104

329

0.93

(0.18)

RF01838

77

69%

4

77

0

1.00

(0.20)

4

77

0

1.00

(0.20)

77

172

1.00

(0.20)

RF02031

164

71%

17

164

297,941

0.99

(0.19)

12

164

521,018

0.99

(0.19)

100

218

0.60

(0.11)

RF00052

210

72%

16

210

0

1.00

(0.20)

12

210

0

1.00

(0.20)

207

12,496

0.98

(0.19)

RF00543

103

73%

26

103

0

1.00

(0.20)

19

103

0

1.00

(0.20)

102

110

0.99

(0.19)

RF01744

14

73%

7

14

0

1.00

(0.20)

5

14

0

1.00

(0.20)

11

5,377

0.74

(0.14)

RF01769

149

75%

16

149

0

1.00

(0.20)

10

149

0

1.00

(0.20)

149

150

0.99

(0.19)

RF00110

161

81%

19

161

0

1.00

(0.20)

17

161

0

1.00

(0.20)

160

791

0.99

(0.19)

RF01967

50

84%

37

50

660,130

0.98

(0.19)

26

50

475,242

0.98

(0.19)

48

691

0.95

(0.19)

RF01472

26

85%

6

26

0

1.00

(0.20)

1

26

0

1.00

(0.20)

26

412

1.00

(0.20)

RF01953

46

85%

32

46

0

1.00

(0.20)

22

46

0

1.00

(0.20)

46

772

1.00

(0.20)

RF00372

45

86%

28

45

0

1.00

(0.20)

24

45

0

1.00

(0.20)

45

197

0.99

(0.19)

RF01980

43

86%

39

43

830,971

0.97

(0.19)

28

43

702,352

0.96

(0.19)

43

341

1.00

(0.20)

RF00469

1,366

89%

12

1,366

46,351

0.99

(0.19)

7

1,366

99,045

0.99

(0.19)

1,341

474

0.97

(0.19)

Average

 

66%

   

0.93

(0.17)

   

0.89

(0.16)

  

0.72

(0.14)

  1. Searches are performed using RaligNAtor with and without base pairing information (column “RaligNAtor (sequence only)”) and using program blastn with the families’ seed alignment consensus sequence as query. Column “size” indicates the number of members in a family. Column “seq. ident.” gives the families’ sequence identity as listed in the Rfam database. #TP and #FP stand for number of found true and false positives, respectively. AUC is the area under the curve of the corresponding ROC curves shown in Figures 11, S7, and S8 of Additional file 1. Column pAUC gives the partial area under the curve up to a false positive rate of 20%. For additional details, see main text.