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Table 1.

Results on the Test Sets

Test set		Nucleotide level		Exon level
Test set		SN	SP	AC	SN	SP	(SN+SP)/2	ME	WE
The ROSETTA set
ROSETTA	0.935	0.978	0.949	0.833	0.829	0.831	0.048	0.047
SGP-1	0.940	0.960	0.940	0.700	0.760	0.730	0.120	0.040
SLAM	0.951	0.981	0.960	0.783	0.755	0.769	0.038	0.057
TWINSCAN.p	0.960	0.941	0.940	0.855	0.824	0.840	0.045	0.081
TWINSCAN	0.984	0.889	0.923	0.839	0.767	0.803	0.034	0.118
GENSCAN	0.975	0.908	0.929	0.817	0.770	0.793	0.057	0.107
HoxA
SLAM	0.852	0.896	0.864	0.727	0.533	0.630	0.000	0.333
TWINSCAN.p	0.976	0.829	0.896	0.773	0.531	0.652	0.000	0.312
TWINSCAN	0.949	0.511	0.704	0.591	0.173	0.382	0.000	0.707
SGP-2	0.640	0.637	0.619	0.409	0.173	0.291	0.091	0.596
GENSCAN	0.932	0.687	0.796	0.545	0.235	0.390	0.000	0.569
Elastin
SLAM	0.876	0.981	0.926	0.802	0.859	0.831	0.121	0.059
TWINSCAN.p	0.942	0.950	0.945	0.879	0.889	0.884	0.066	0.056
TWINSCAN	0.933	0.877	0.903	0.835	0.826	0.831	0.110	0.120
SGP-2	0.755	0.998	0.873	0.593	0.900	0.291	0.352	0.017
GENSCAN	0.947	0.766	0.852	0.835	0.731	0.783	0.121	0.231

[i] The measures of sensitivity SN = TP/TP + FN and specificity SP = TP/TP + FP (where TP = true positives, TN = true negatives, FP = false positives and FN = false negatives) are shown at both the nucleotide and exon level. ME is entirely missed exons, WE is wrong exons, and the approximate correlation AC = 1/2 (TP/TP + FN + TP/TP + FP + TN/TN + FP + TN/TN + FN) − 1 summarizes the overall nucleotide sensitivity and specificity by one number. Within each of the three data sets the methods are divided into three classes: those operating on a syntenic DNA pair, those operating on a human sequence using as evidence matches against a database of mouse sequences, and a single-organism gene finder (GENSCAN).