Table 1. Accuracy results on a 2.9 million bp long sequence from the Drosophila Adh region.

Program	Base level		Exon level		Gene level
	Sensitivity (%)	Specificity (%)	Sensitivity (%)	Specificity (%)	Sensitivity (%)	Specificity (%)
AUGUSTUS	98	93	85	65	68	38
GENEID	96	92	71	62	47	33
GENIE	96	92	70	57	40	29

For each of the three programs the sensitivity was measured using a set of annotations, called std1, which contains 38 genes. The specificity was measured using another set of annotations, called std3, which contains 222 genes. For testing we used release 2 of AUGUSTUS and version 1.1 of GENEID. The results for GENIE were taken from (11).