Markup | Genome Research

Table 3.

Evaluation of Gene-Finding Systems

		`FGenes 1`	FGenes 2	FGenes 3	GeneID v1	GeneID v2	Genie	Genie EST	Genie ESTHOM	HMMGene	MAGPIE exon	GRAIL
Base level	Sn std1	0.89	0.49	0.93	0.48	0.86	0.96	0.97	0.97	0.97	0.96	0.81
	Sp std3	0.77	0.86	0.60	0.84	0.83	0.92	0.91	0.83	0.91	0.63	0.86
Exon level	Sn std1	0.65	0.44	0.75	0.27	0.58	0.70	0.77	0.79	0.68	0.63	0.42
	Sp std3	0.49	0.68	0.24	0.29	0.34	0.57	0.55	0.52	0.53	0.41	0.41
	ME (%) std1	10.5	45.5	5.6	54.4	21.1	8.1	4.8	3.2	4.8	12.1	24.3
	WE (%) std3	31.6	17.2	53.3	47.9	47.4	17.4	20.1	22.8	20.2	50.2	28.7
Gene level	Sn std1	0.30	0.09	0.37	0.02	0.26	0.40	0.44	0.44	0.35	0.33	0.14
	Sp std3	0.27	0.18	0.10	0.05	0.10	0.29	0.28	0.26	0.30	0.21	0.12
	MG (%) std1	9.3	34.8	9.3	44.1	13.9	4.6	4.6	4.6	6.9	4.6	16.2
	WG (%) std3	24.3	24.8	52.3	22.2	30.5	10.7	13.0	15.5	14.9	55.0	23.7
	SG	1.10	1.10	2.11	1.06	1.06	1.17	1.15	1.16	1.04	1.22	1.23
	JG	1.06	1.09	1.08	1.62	1.11	1.08	1.09	1.09	1.12	1.06	1.08

[i] The evaluation is divided into three categories: base level, exon level, and gene level. The different statistical features reported are Sn, Sp, ME, WE, MG, WG, SG, and JG. std1 and std3 indicate against which standard set the statistics are reported.