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Table 1 In silico analysis of restriction enzyme cutting statistics for the human reference genome (hg19)

From: Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line

Enzyme

Usable DNA fragments (%)

Average fragment size (kb)

Maximum fragment size (kb)

#Fragments >100 kb

 

5–20 kb

6–15 kb

6–12 kb

AflII

13.3

5.48

5.43

4.47

143.96

4

BamHI

99.22

92.95

92.9

7.92

153.92

21

Kpn I

99.95

99.88

99.51

9.98

171.76

65

NcoI

0.08

0.03

0.03

3.81

164.18

2

NheI

99.86

98.97

90.75

10.23

204.75

88

SpeI

99.28

96.71

94.55

7.27

311.48

101

BglII

2.33

0.81

0.8

3.71

109.69

1

EcoRI

2.21

0.79

0.79

3.67

86.14

0

MluI

0.34

0.01

0.01

135.32

2276.59

8295

NdeI

5.9

1.78

1.78

3.19

105.86

1

PvuII

0.03

0.02

0.02

2.66

173.76

6

XbaI

2.75

1.15

1.15

3.58

146.27

2

XhoI

17.02

6.37

2.21

23.78

430.88

3269

  1. To select the restriction enzyme that cuts the human genome to maximize the fraction of fragments resulting in informative maps, the human genome was cut in silico with 13 commonly used restriction enzymes based on their canonical cutting sites. Usable restriction fragment sizes were defined as 5–20 kb, 6–15 kb, and 6–12 kb, since smaller DNA fragments do not allow accurate size estimates, and longer fragments can result in maps with too few fragments. KpnI was selected based on its high fraction of usable DNA fragments (highlighted in bold)