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Table 4 Cross-correlations between experimental and standard digital T-RFLP profiles

From: PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Samples

Optimal cross-correlation lag between digital and experimental T-RFLP profilesa(bp)

Maximum cross-correlation coefficient at optimal lagb(−)

Total number of experimental T-RFs per profile (−)

Number of experimental T-RFs affiliated with digital T-RFsc(−)

Percentage of experimental T-RFs affiliated with digital T-RFsc(%)

Groundwater

     

GRW01d

−4

0.62

88

58

66

GRW02d

−5

0.69

50

23

46

GRW03d

−4

0.44

76

62

82

GRW04d

−5

0.71

44

24

44

GRW05d

−5

0.35

75

56

75

GRW06d

−6

0.51

87

70

81

Avg±stdev (min-max)

−5±1

0.55±0.14

70±19

49±20

67±14

-(4–6)

(0.35-0.71)

(44–88)

(23–70)

(44–82)

GRW07e

−6

0.70

57

17

30

GRW08e

−4

0.59

54

43

80

GRW09e

−4

0.69

71

66

93

GRW10e

−5

0.68

70

22

31

Avg±stdev (min-max)

−5±1

0.67±0.05

59±11

34±20

59±33

 

-(4–6)

(0.59-0.70)

(44–71)

(17–66)

(30–93)

Aerobic granular sludge

AGS01e

−5

0.75

48

31

65

AGS02e,f

−5

0.90

38

22

58

AGS03e,f

−5

0.90

38

19

50

AGS04e

−5

0.72

52

24

46

AGS05e

−4

0.67

43

29

67

AGS06e,f

−5

0.91

38

19

50

AGS07e

−5

0.80

38

31

82

Avg±stdev (min-max)

−5±0

0.82±0.10

42±6

25±5

61±12

 

-(4–5)

(0.67-0.91)

(38–52)

(19–31)

(46–82)

  1. a Shift leading to optimal matching of the digital to the experimental T-RFLP profile.
  2. b Maximum cross-correlation coefficients obtained after matching of the digital to the experimental T-RFLP profile.
  3. c Number and percentage of experimental T-RFs having corresponding digital T-RFs.
  4. d Samples GRW01-06 were pyrosequenced with the HighRA method.
  5. e Samples GRW07-10 and AGS01-07 were pyrosequenced with the LowRA method.
  6. f Samples AGS02, AGS03, and AGS06 are triplicates from the same DNA extract.