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Table 2.

Distribution of the gene-prediction candidates among the four groups that differ by the level of extrinsic support

Species	Support for predicted gene candidates	Order excluded DB		Species excluded DB
Species	Support for predicted gene candidates	No. of candidates	Precision %	No. of candidates	Precision %
C. elegans	Fully extrinsic	7676	88.9	10,778	91.6
	Partially extrinsic	4804	56.4	5417	54.4
	Match to low-scoring hints	4020	54.7	1548	45.2
	No extrinsic match	1298	24.9	778	18.0
A. thaliana	Fully extrinsic	16,445	97.2	18,083	97.5
	Partially extrinsic	4825	64.4	5807	55.7
	Match to low-scoring hints	1794	50.2	1360	30.1
	No extrinsic match	2964	27.9	1128	9.4
D. melanogaster	Fully extrinsic	8059	95.1	9952	96.8
	Partially extrinsic	2328	49.3	2751	44.9
	Match to low-scoring hints	1043	57.1	165	44.9
	No extrinsic match	1369	41.6	377	15.9
S. lycopersicum	Fully extrinsic	17,639	95.2	18,420	95.0
	Partially extrinsic	5174	47.3	5813	44.3
	Match to low-scoring hints	1577	38.4	1484	29.7
	No extrinsic match	4714	14.8	3703	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	1973	11.4	1663	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	4857	19.6	5337	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	7376	20.6	7606	19.6
	Match to low-scoring hints	957	10.1	1155	7.3
	No extrinsic match	20,711	1.2	19,666	0.5

[i] In the “match to low-scoring hints” category, we placed the candidates that were predicted fully ab initio, whereas 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.”