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Table 1.

Evaluation of Gene Prediction Accuracy

Test set		Nucleotide level		Exon level
Test set		S_n	S_p	AC	S_N	S_P	( S_N + S_P )/2	ME	WE
SetS1 (human/rodent single genes)
SGP`SIM` [i]	0.94	0.96	0.94	0.70	0.76	0.73	0.12	0.04
SGP`TBLASTX` [i]	0.87	0.96	0.90	0.64	0.73	0.68	0.15	0.03
`Rosetta` [ii]	0.95	0.97	0.96	0.84	0.84	0.84	0.04	0.05
`Genscan`	0.97	0.89	0.92	0.79	0.74	0.76	0.06	0.13
SetS2 (human/rodent multiple genes)
ERCC2
SGP`SIM`	0.91	0.96	0.93	0.72	0.80	0.76	0.15	0.06
SGP`TBLASTX`	0.89	0.97	0.92	0.69	0.84	0.77	0.18	0.00
`Genscan`	0.99	0.71	0.83	0.79	0.70	0.74	0.05	0.16
MHC
SGP`SIM`	0.79	0.99	0.88	0.60	0.80	0.70	0.28	0.02
SGP`TBLASTX`	0.67	1.00	0.83	0.45	0.69	0.57	0.38	0.00
`Genscan`	0.93	0.73	0.82	0.72	0.58	0.65	0.14	0.31
HOX
SGP`SIM`	0.86	0.86	0.85	0.62	0.50	0.56	0.10	0.23
SGP`TBLASTX`	0.51	0.91	0.69	0.24	0.33	0.29	0.33	0.07
`Genscan`	0.94	0.77	0.85	0.67	0.30	0.44	0.05	0.47
MeCP2
SGP`SIM`	0.99	0.93	0.96	0.92	0.89	0.91	0.08	0.11
SGP`TBLASTX`	0.72	0.85	0.78	0.46	0.50	0.48	0.19	0.21
`Genscan`	0.97	0.73	0.83	0.80	0.73	0.76	0.07	0.21
Set T1 (plant single genes)
SGP`SIM`	0.93	0.99	0.94	0.57	0.63	0.60	0.12	0.00
SGP`TBLASTX`	0.88	0.97	0.91	0.64	0.76	0.70	0.18	0.00
`Genscan`	0.92	0.90	0.87	0.61	0.57	0.59	0.09	0.15

[i] Alignment of SGP-1 with SIM96 (DNA alignment) and with TBLASTX (amino acid alignment).

[ii] Rosetta results on S1 provided by S. Batzoglou; results on S2 and T1 are not available.