Table 2.

Distribution of the intermediate sets of predicted genes among the four categories characterized by the degree of connection to extrinsic data.

Species	Gene predictions	Smaller protein DB		Larger protein DB
		# of genes	Specificity, %	# of genes	Specificity, %
C. elegans	Fully extrinsic	7,676	88.9	10,778	91.6
	Partially extrinsic	4,804	56.4	5,417	54.4
	With extrinsic match	4,020	54.7	1,548	45.2
	With no extrinsic match	1,298	24.9	778	18.0
A. thaliana	Fully extrinsic	16,445	97.2	18,083	97.5
	Partially extrinsic	4,825	64.4	5,807	55.7
	With extrinsic match	1,794	50.2	1,360	30.1
	With no extrinsic match	2,964	27.9	1,128	9.4
D. melanogaster	Fully extrinsic	8,059	95.1	9,952	96.8
	Partially extrinsic	2,328	49.3	2,751	44.9
	With extrinsic match	1,043	57.1	165	44.9
	With no extrinsic match	1,369	41.6	377	15.9
S. lycopersicum	Fully extrinsic	17,639	95.2	18,420	95.0
	Partially extrinsic	5,174	47.3	5,813	44.3
	With extrinsic match	1,577	38.4	1,484	29.7
	With no extrinsic match	4,714	14.8	3,703	9.2
D. rerio	Fully extrinsic	15,691	89.8	15,501	92.6
	Partially extrinsic	10,905	16.6	11,769	16.6
	With extrinsic match	1,973	11.4	1,663	7.3
	With no extrinsic match	12,534	0.8	11,879	0.3
G. gallus	Fully extrinsic	11,856	89.3	11,547	89.9
	Partially extrinsic	4,857	19.6	5,337	20.1
	With extrinsic match	527	8.9	579	7.1
	With no extrinsic match	11,332	0.4	11,352	0.3
M. musculus	Fully extrinsic	13,556	94.6	13,769	96.2
	Partially extrinsic	7,376	20.6	7,606	19.6
	With extrinsic match	957	10.1	1,155	7.3
	With no extrinsic match	20,711	1.2	19,666	0.5

The average Sp values (gene level) are given for the genes of each category. Descriptions of the species-specific protein databases (the smaller one – ‘Order excluded’ and the larger one – ‘Species excluded’) are given in Materials.