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

Table 3.

Performance of Ab Initio Programs on Burset/Guigo (1996) 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	8	0.93	0.91	0.92	0.90	2156	264	26	203	188	0.78	0.79	0.79
GENSCAN+BLASTX	0	0.98	0.91	0.94	0.93	2299	230	28	100	305	0.84	0.80	0.82
GENSCAN+BLASTX+BLASTN	0	0.98	0.93	0.94	0.94	2301	222	22	112	250	0.84	0.82	0.83
HMMgene	38	0.87	0.88	0.91	0.86	2092	239	21	308	139	0.76	0.77	0.77
HMMgene+BLASTX	2	0.95	0.95	0.94	0.94	2256	248	21	135	144	0.83	0.83	0.83
HMMgene+BLASTX+BLASTN	2	0.95	0.96	0.95	0.94	2252	234	17	154	97	0.83	0.84	0.84
EUI	20	0.90	0.92	0.93	0.90	2214	176	12	250	98	0.80	0.84	0.82
EUI+BLASTX	0	0.96	0.96	0.95	0.95	2297	213	14	129	106	0.84	0.86	0.85
EUI+BLASTX+BLASTN	0	0.96	0.97	0.95	0.95	2294	205	12	142	79	0.84	0.87	0.85
EUI-FRAME	27	0.88	0.92	0.92	0.88	2188	167	11	286	87	0.79	0.84	0.81
EUI-FRAME+BLASTX	1	0.96	0.96	0.95	0.95	2286	214	13	140	95	0.84	0.86	0.85
EUI-FRAME+BLASTX+BLASTN	1	0.95	0.97	95.00	0.90	2283	206	12	152	69	0.83	0.87	0.85
GI	43	0.84	0.90	0.91	0.85	2118	138	8	387	67	0.76	0.83	0.80
GI+BLASTX	2	0.95	0.97	0.95	0.95	2277	195	10	167	76	0.83	0.87	0.85
GI+BLASTX+BLASTN	2	0.94	0.97	0.94	0.94	2274	190	9	178	52	0.83	0.88	0.85
GENOMESCAN	12	0.95	0.89	0.92	0.90	2245	235	45	130	350	0.81	0.78	0.80

This Article

Genome Res. 2004. 14: 1756-1766

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