Table 4

Performance on the EGASP test regions. Sensitivity (Sn) and specificity (Sp) are shown at the nucleotide (Nuc), exon, transcript (Trans) and gene levels for CONTRAST and the 19 predictors entered in the EGASP experiment. At each level of evaluation, the performance of the predictor with the highest average sensitivity and specificity for a given category is shown in bold. Also shown is the performance of the UCSC RefGene track, which consists of RefSeq cDNAs aligned to the genome. The track was evaluated just before the start of the EGASP workshop.

Nuc Sn

Nuc Sp

Exon Sn

Exon Sp

Trans Sn

Trans Sp

Gene Sn

Gene Sp


RefGene Track

85.34

98.50

73.23

94.67

41.91

75.21

77.03

82.56

Category 1 (any information)

AUGUSTUS-any

94.42

82.43

74.67

76.76

22.65

35.59

47.97

35.59

FGENESH++

91.09

76.89

75.18

69.31

36.21

41.61

69.93

42.09

JIGSAW

94.56

92.19

80.61

89.33

34.05

65.95

72.64

65.95

PAIRAGON-any

87.77

92.78

76.85

88.91

39.29

60.34

69.59

61.32

Category 2 (target sequence)

AUGUSTUS-abinit

78.65

75.29

52.39

62.93

11.09

17.22

24.32

17.22

GENEMARK.hmm-A

78.43

37.97

50.58

29.01

6.93

3.24

15.20

3.24

GENEMARK.hmm-B

76.09

62.94

48.15

47.25

7.70

7.91

16.89

7.91

GENEZILLA

87.56

50.93

62.08

50.25

9.09

8.84

19.59

8.84

Category 3 (protein, mRNA, EST)

ACEVIEW

90.94

79.14

85.75

56.98

44.68

19.31

63.51

48.65

AUGUSTUS-EST

92.62

83.45

74.10

77.40

22.50

37.01

47.64

37.01

ENSEMBL

90.18

92.02

77.53

82.65

39.75

54.64

71.62

67.32

EXOGEAN

84.18

94.33

79.34

83.45

42.53

52.44

63.18

80.82

EXONHUNTER

90.46

59.67

64.44

41.77

10.48

6.33

21.96

6.33

PAIRAGON+NSCAN_EST

87.56

92.77

76.63

88.95

39.29

60.64

69.59

61.71

Category 4 (genomic alignments)

CONTRAST

94.44

89.25

77.68

86.02

25.12

47.87

53.04

47.87

AUGUSTUS-dual

88.86

80.15

63.06

69.14

12.33

18.64

26.01

18.64

DOGFISH

64.81

88.24

53.11

77.34

5.08

14.61

10.81

14.61

MARS

84.25

74.13

65.56

61.65

15.87

15.11

33.45

24.94

NSCAN

85.38

89.02

67.66

82.05

16.95

36.71

35.47

36.71

SAGA

52.54

81.39

38.82

50.73

2.16

3.44

4.39

3.44


Gross et al. Genome Biology 2007 8:R269   doi:10.1186/gb-2007-8-12-r269

Open Data