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Table 4 Effects of individual restriction enzymes on cDNA-pool coverage.

From: Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

Source

(Restriction Site)

df

SS I

F

Sig.

Coverage Estimate

CviAII (C^ATG)

1

121.08

4806.32

<0.001

43.63

MseI (T^TAA)

1

153.42

6090.19

<0.001

32.49

CviQI (G^TAC)

1

69.09

2742.53

<0.001

31.06

TaqI (T^CGA)

1

52.69

2091.52

<0.001

30.20

MaeI (C^TAG)

1

63.15

2506.75

<0.001

25.79

MaeII (A^CGT)

1

86.56

3436.05

<0.001

24.66

HpaII (C^CGG)

1

136.20

5406.74

<0.001

23.34

HinP1I (G^CGC)

1

137.28

5449.32

<0.001

17.12

Enzyme combination

20

0.78

1.55

0.056

n/a

  1. The effects of individual restriction enzymes on cDNA-pool coverage, based on all 92 species (Table 3; see additional file 1). The percentage of total cDNA pool coverage explained by each enzyme has been estimated. The degrees of freedom (df) of each factor included in the model (source) are indicated. Enzymes are sorted by decreasing coverage, and restriction sites of each restriction enzyme are listed. Details on the significance of each factor (Sig.) in this analysis and corresponding F-statistics are given (see Methods).