Table 4

Performance of foreign and bootstrapped parameters The foreign parameter data (top part of the table) is similar to table 4 but use the default rather than tuned architectures (see Methods). The bold face values are determined by 5-fold cross-validation within the same species. At Arabidopsis thaliana, Ce Caenorhabditis elegans, Dm Drosophila melanogaster, Os Oryza sativa. Sensitivity (NSN) and specificity (NSP) are reported at the nucleotide level. The bootstrapped values (bottom part of the table) are derived from parameter estimates based on gene predictions and no actual data. In these experiments, only inter-species gene parameters were used; dashes represent cells that would contain intra-species predictions.

Genomic DNA

At

Ce

Dm

Os

Parameters

NSN

NSP

NSN

NSP

NSN

NSP

NSN

NSP


Actual

At

97.6

94.3

81.0

90.1

75.3

63.6

90.7

68.5

Ce

86.3

91.0

98.1

92.5

85.1

72.4

79.8

73.0

Dm

26.0

96.0

38.6

96.0

93.8

87.0

76.1

89.8

Os

36.0

96.9

21.7

96.1

78.5

88.7

85.1

94.2


Bootstrapped

At

-

-

95.8

88.2

94.7

76.0

92.1

76.0

Ce

96.6

93.2

-

-

95.7

80.3

91.0

79.2

Dm

75.2

95.5

90.0

94.9

-

-

74.1

88.7

Os

85.6

95.8

76.5

94.3

92.5

86.6

-

-

At Ce

-

-

-

-

95.7

78.3

92.8

77.8

At Dm

-

-

96.7

91.1

-

-

85.4

80.9

At Os

-

-

95.5

90.3

94.0

81.2

-

-

Ce Dm

94.3

94.4

-

-

-

-

84.0

83.0

Ce Os

94.5

94.6

-

-

94.7

83.3

-

-

Dm Os

84.9

95.8

88.4

94.9

-

-

-

-

At Ce Dm

-

-

-

-

-

-

88.1

80.2

At Ce Os

-

-

-

-

95.2

80.9

-

-

At Dm Os

-

-

95.8

91.9

-

-

-

-

Ce Dm Os

93.4

95.1

-

-

-

-

-

-


Korf BMC Bioinformatics 2004 5:59   doi:10.1186/1471-2105-5-59

Open Data