Table 4

CDS assessment: summary of accuracy measures for CDS features at the nucleotide and exon levels

Nucleotide

Exon



NSn

NSp

N CC

ESn

ESp

ME

WE


Category 1

AUGUSTUS-any

94.42%

82.43%

0.88

74.67%

76.76%

8.25%

16.29%

FGENESH++

91.09%

76.89%

0.83

75.18%

69.31%

9.73%

24.64%

JIGSAW

94.56%

92.19%

0.93

80.61%

89.33%

6.22%

7.78%

PAIRAGON-any

87.77%

92.78%

0.90

76.85%

88.91%

11.18%

6.82%

Category 2

AUGUSTUS-abinit

78.65%

75.29%

0.76

52.39%

62.93%

29.09%

24.82%

GENEMARK.hmm-A

78.43%

37.97%

0.53

50.58%

29.01%

27.86%

63.27%

GENEMARK.hmm-B

76.09%

62.94%

0.69

48.15%

47.25%

31.77%

40.68%

GENEZILLA

87.56%

50.93%

0.66

62.08%

50.25%

19.14%

41.93%

Category 3

ACEVIEW

90.94%

79.14%

0.84

85.75%

56.98%

4.38%

16.69%

AUGUSTUS-EST

92.62%

83.45%

0.88

74.10%

77.40%

9.01%

15.61%

ENSEMBL

90.18%

92.02%

0.91

77.53%

82.65%

9.99%

9.22%

EXOGEAN

84.18%

94.33%

0.89

79.34%

83.45%

9.88%

5.06%

EXONHUNTER

90.46%

59.67%

0.73

64.44%

41.77%

14.29%

50.94%

PAIRAGON+NSCAN_EST

87.56%

92.77%

0.90

76.63%

88.95%

11.51%

6.85%

Category 4

AUGUSTUS-dual

88.86%

80.15%

0.84

63.06%

69.14%

16.82%

19.60%

DOGFISH

64.81%

88.24%

0.74

53.11%

77.34%

32.67%

11.70%

MARS

84.25%

74.13%

0.78

65.56%

61.65%

20.26%

26.10%

NSCAN

85.38%

89.02%

0.87

67.66%

82.05%

17.11%

10.93%

SAGA

52.54%

81.39%

0.65

38.82%

50.73%

40.48%

27.85%

UCSC Tracks

ACEMBLY

96.43%

58.47%

0.74

84.66%

38.32%

2.71%

28.55%

CCDSgene

56.87%

99.52%

0.75

51.95%

97.75%

40.38%

0.27%

ECgene

96.36%

47.30%

0.66

86.22%

35.08%

2.64%

45.92%

ENSgene

91.39%

91.92%

0.92

77.71%

82.39%

9.80%

9.21%

GENEID

76.77%

76.48%

0.76

53.84%

61.08%

27.86%

27.26%

GENSCAN

84.17%

60.60%

0.71

58.65%

46.37%

19.50%

42.91%

KNOWNgene

89.10%

93.61%

0.91

78.11%

82.28%

10.27%

4.30%

MGCgene

44.06%

97.56%

0.65

42.95%

93.61%

49.28%

2.68%

REFgene

85.34%

98.50%

0.92

73.23%

94.67%

15.38%

1.22%

SGPgene

82.81%

82.20%

0.82

60.56%

65.16%

19.36%

22.85%

TWINSCAN

78.16%

84.59%

0.81

58.43%

73.11%

24.64%

16.30%


CC, correlation coefficient.

Guig√≥ et al. Genome Biology 2006 7(Suppl 1):S2   doi:10.1186/gb-2006-7-s1-s2