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Table 1 The numbers of annotated and additional genes found by ZCURVE_V and GeneMark gene-finding family, respectively, for 30 viral genomes with different chromosome lengths a

From: ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes

GenBank information

ZCURVE_V

GeneMarkb

Glimmer d

Organisms

Sequence length (bp)

GC content

No. of annotated genes

No. of predicted genes

S n

S p

No. of predicted genes

S n

S p

No. of predicted genes

S n

S p

CNPV

359,853

30.37

328

342

99.4

95.3

327

97.9

98.2

351

99.1

92.6

FPV

288,539

30.89

261

282

95.4

88.3

257

93.5

94.9

307

95.0

80.8

THV

195,859

66.61

158

199

90.5

71.9

109

57.6

83.5

207

50.6

38.6

ASFV

170,101

38.95

151

164

96.0

88.4

148

93.4

95.3

185

95.4

77.8

MYXV

161,773

43.56

170

170

98.8

98.8

172

97.6

96.5

180

98.2

92.8

SFV

159,857

39.53

165

170

96.4

93.5

168

97.0

95.2

188

98.2

86.2

YLDV

144,575

27.00

152

156

99.3

96.8

155

98.7

96.8

165

98.7

90.9

ORFV

139,962

63.44

130

131

92.3

91.6

133

91.5

89.5

187

97.7

67.9

BPSV

134,431

64.50

131

144

96.9

88.2

135

93.9

91.1

150

86.3

75.3

AcNPV

133,894

40.70

155

155

97.4

97.4

152

94.8

96.7

174

96.2

86.2

BmNPV

128,413

40.40

143

139

97.2

100

139

95.1

97.8

157

95.8

87.3

PhopGV

119,217

35.7

130

132

96.2

94.7

130

93.1

93.1

168

96.9

75.0

AdhoNPV

113,220

35.64

125

121

92.0

95.0

125

94.4

94.4

143

95.2

83.2

LCDV-1

102,653

29.07

110

112

97.3

95.5

110

96.4

96.4

114

98.2

94.7

PxGV

100,999

40.69

120

116

93.3

96.6

123

92.5

90.2

131

94.2

86.3

AdorGV

99,657

34.49

119

121

97.5

95.9

116

94.1

96.6

137

95.8

83.2

NeleNPV

81,755

33.31

93

101

92.5

85.1

73

75.3

95.9

125

91.4

68.0

FAdV-9

45,063

53.78

29

48

100

60.4

35

96.6

80

60

100

48.3

PAdV-5

32,621

50.50

30

35

90.0

77.1

27

76.7

85.2

39

90.0

69.2

IBV

27,608

37.93

10

10

90.0

90.0

7

70

100

10

70.0

70.0

CTV

19,296

45.27

11

11

100

100

8

72.7

100

12

90.9

83.3

SHFV

15,717

50.11

11

11

100

100

8

54.5

75

--

--

--

BYV

15,480

46.03

8

8

100

100

7

87.5

100

11

100

72.7

FDLV

15,378

43.13

8

8

100

100

8

100

100

11

100

72.7

EAV

12,704

51.66

9

9

88.8

88.8

6

55.5

83.3

11

77.8

63.6

SFV

11,442

53.22

2

2

100

100

2

100

100

--

--

--

BCMV

9612

42.22

1

1

100

100

2

100

50

3

100

33.3

GLV

8363

43.86

6

6

100

100

4

66.7

100

7

50

42.9

FMV

7743

35.36

7

7

100

100

7

100

100

7

100

100

SCMV

4194

51.55

4

3

75

100

2

50

100

2

50

100

Average (upper 15)c

-

-

-

-

95.9 95.9

92.8

-

92.5

94.0

-

93.05

81.0

Average (lower 15)c

-

-

-

-

95.6

93.2

-

80.0

91.1

-

85.84

69.8

Average (30)c

-

-

-

-

95.7

93.0

-

86.2

92.5

-

89.70

75.8

  1. a The names of the viruses are listed in the descending order of their chromosome sequence lengths. The abbreviation names of viruses are used. See the text for the detail.
  2. b For the genomes of canarypox virus (CNPV), orf virus (ORFV), bovine papular stomatitis virus (BPSV) and neodiprion lecontei nucleopolyhedrovirus (NeleNPV), genes were predicted directly by GeneMarks program, whereas for the other 26 viral genomes the data deposited in the GeneMark VIOLIN database are used.
  3. c The values are averaged over the upper 15, lower 15 and all the 30 viral genomes, respectively.
  4. d Glimmer 2.02 predicted no genes for simian hemorrhagic fever virus (SHFV) and semliki forest virus (SFV) genomes.