Table 2.

Distribution of the gene prediction candidates among the four groups that differ by the level of extrinsic support. In the ‘Match to low scoring hints’ category we placed the candidates that were predicted fully ab initio while in a posteriori analysis a match of at least one exon border to a low scoring extrinsic hint was detected. The category ‘No extrinsic match’ contains the ab initio predictions that have no match to any extrinsic hints (see text). Average gene level Pr values are listed for each group. Protein databases are described in the section Data Sets.

Species	Support for predicted gene candidates	Order excluded DB		Species excluded DB
		# of candidates	Precision %	# of candidates	Precision %
C. elegans	Fully extrinsic	7,676	88.9	10,778	91.6
	Partially extrinsic	4,804	56.4	5,417	54.4
	Match to low scoring hints	4,020	54.7	1,548	45.2
	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
	Match to low scoring hints	1,794	50.2	1,360	30.1
	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
	Match to low scoring hints	1,043	57.1	165	44.9
	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
	Match to low scoring hints	1,577	38.4	1,484	29.7
	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
	Match to low scoring hints	1,973	11.4	1,663	7.3
	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
	Match to low scoring hints	527	8.9	579	7.1
	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
	Match to low scoring hints	957	10.1	1,155	7.3
	No extrinsic match	20,711	1.2	19,666	0.5