EGPred: Prediction of Eukaryotic Genes Using Ab Initio Methods After Combining With Sequence Similarity Approaches

Table 2.

Performance of Ab Initio Programs on HMR195 Data Set on Adding Similarity Information

		Nucleotide level							Exon level
Program	No. genes	SEN	SPE	AC	CC	CR	PC	OL	ME	WE	ESEN	ESPE	EAVG
GENSCAN	3	0.93	0.89	0.91	0.89	735	131	10	76	104	0.70	0.69	0.70
GENSCAN+BLASTX	0	0.98	0.89	0.92	0.92	799	110	11	36	176	0.81	0.73	0.77
GENSCAN+BLASTX+BLASTN	0	0.97	0.90	0.92	0.92	801	101	9	45	163	0.81	0.74	0.78
HMMgene	5	0.90	0.90	0.91	0.89	715	98	11	128	81	0.74	0.75	0.75
HMMgene+BLASTX	0	0.95	0.93	0.93	0.93	779	91	15	68	91	0.80	0.78	0.79
HMMgene+BLASTX+BLASTN	0	0.95	0.95	0.94	0.93	780	86	13	74	74	0.80	0.80	0.80
EUI	3	0.92	0.94	0.93	0.91	769	74	4	104	55	0.77	0.81	0.79
EUI+BLASTX	0	0.96	0.94	0.94	0.94	795	86	8	63	65	0.80	0.81	0.81
EUI+BLASTX+BLASTN	0	0.95	0.96	0.95	0.94	795	81	7	69	53	0.80	0.83	0.82
EUI-FRAME	3	0.92	0.94	0.93	0.91	762	70	5	115	46	0.77	0.82	0.79
EUI-FRAME+BLASTX	0	0.96	0.95	0.94	0.94	793	84	9	67	56	0.80	0.82	0.81
EUI-FRAME+BLASTX+BLASTN	0	0.95	0.96	0.95	0.94	793	79	8	73	48	0.80	0.83	0.82
GI	15	0.84	0.89	0.90	0.84	742	57	3	149	43	0.72	0.80	0.76
GI+BLASTX	0	0.95	0.95	0.94	0.94	796	78	7	71	56	0.80	0.83	0.82
GI+BLASTX+BLASTN	0	0.94	0.97	0.94	0.94	796	70	6	77	45	0.80	0.85	0.83
GENOMESCAN	1	0.96	0.87	0.91	0.90	781	115	16	45	213	0.78	0.71	0.74

This Article

Genome Res. 2004. 14: 1756-1766

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