Table 4.

Performance on the EGASP test regions. Sensitivity (Sn) and specificity (Sp) are shown at the nucleotide (Nuc), exon, transcript (Trans) and gene levels for CONTRAST and the 19 predictors entered in the EGASP experiment. At each level of evaluation, the performance of the predictor with the highest average sensitivity and specificity for a given category is shown in bold. Also shown is the performance of the UCSC RefGene track, which consists of RefSeq cDNAs aligned to the genome. The track was evaluated just before the start of the EGASP workshop.

	Nuc Sn	Nuc Sp	Exon Sn	Exon Sp	Trans Sn	Trans Sp	Gene Sn	Gene Sp
RefGene Track	85.34	98.50	73.23	94.67	41.91	75.21	77.03	82.56
Category 1 (any information)
AUGUSTUS-any	94.42	82.43	74.67	76.76	22.65	35.59	47.97	35.59
FGENESH++	91.09	76.89	75.18	69.31	36.21	41.61	69.93	42.09
JIGSAW	94.56	92.19	80.61	89.33	34.05	65.95	72.64	65.95
PAIRAGON-any	87.77	92.78	76.85	88.91	39.29	60.34	69.59	61.32
Category 2 (target sequence)
AUGUSTUS-abinit	78.65	75.29	52.39	62.93	11.09	17.22	24.32	17.22
GENEMARK.hmm-A	78.43	37.97	50.58	29.01	6.93	3.24	15.20	3.24
GENEMARK.hmm-B	76.09	62.94	48.15	47.25	7.70	7.91	16.89	7.91
GENEZILLA	87.56	50.93	62.08	50.25	9.09	8.84	19.59	8.84
Category 3 (protein, mRNA, EST)
ACEVIEW	90.94	79.14	85.75	56.98	44.68	19.31	63.51	48.65
AUGUSTUS-EST	92.62	83.45	74.10	77.40	22.50	37.01	47.64	37.01
ENSEMBL	90.18	92.02	77.53	82.65	39.75	54.64	71.62	67.32
EXOGEAN	84.18	94.33	79.34	83.45	42.53	52.44	63.18	80.82
EXONHUNTER	90.46	59.67	64.44	41.77	10.48	6.33	21.96	6.33
PAIRAGON+NSCAN_EST	87.56	92.77	76.63	88.95	39.29	60.64	69.59	61.71
Category 4 (genomic alignments)
CONTRAST	94.44	89.25	77.68	86.02	25.12	47.87	53.04	47.87
AUGUSTUS-dual	88.86	80.15	63.06	69.14	12.33	18.64	26.01	18.64
DOGFISH	64.81	88.24	53.11	77.34	5.08	14.61	10.81	14.61
MARS	84.25	74.13	65.56	61.65	15.87	15.11	33.45	24.94
NSCAN	85.38	89.02	67.66	82.05	16.95	36.71	35.47	36.71
SAGA	52.54	81.39	38.82	50.73	2.16	3.44	4.39	3.44