Table 1.

Prediction of motifs by the six programs in the synthetic datasets

Datasets	D1 (500a)		D2 (1000)		D3 (2000)		D4 (5000)		D5 (10 000)		D6 (20 000)		Total true motifs found	Total false motifs found	SN	PPV	PC	FDR	FNR
	True motifs	Discovered motifs	True motifs	Discovered motifs	True motifs	Discovered motifs	True motifs	Discovered motifs	True motifs	Discovered motifs	True motifs	Discovered motifs
ProSampler	10	10	10	10	10	10	10	10	10	10	10	15	60	5	1.00	0.92	0.92	0.08	0.00
BioProspector	10	150	10	150	9	150	9	150	8	150	10	150	56	844	0.93	0.06	0.06	0.94	0.07
DREME	10	14	10	20	10	23	10	36	10	48	10	58	60	139	1.00	0.30	0.30	0.70	0.00
XXmotif	10	17	10	10	10	11	10	11	10	12	10	11	60	12	1.00	0.83	0.83	0.17	0.00
Homer	9	300	10	300	10	300	10	300	10	300	10	300	59	1741	0.98	0.03	0.03	0.97	0.02
motifRG	10	40	8	95	10	91	8	133	7	196	9	150	52	653	0.87	0.07	0.07	0.93	0.13

^aNumber of sequences in the dataset.