MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes

Table 1 Results of the small-scale evaluation.

Factor	Sites	Method	Model	Distinct sequences identified	Target	True positives	False positives	False positive ratio
E2F	27	HMMER	M00050	27	27	36	8	18.20%
			T05206	27	27	27	4	12.90%
		Match	V$E2F_02	27	27	36	7	16.30%
		Patser	V$E2F_02	27	27	36	8	18.20%
		LMM	V$E2F_02	18	27	18	3	n/a
		ScanACE	M00050	12	27	12	3	n/a
ER	17	HMMER	M00959	16	16	22	7	24.10%
			T00258	17	16	16	2	11.10%
		Match	V$ER_Q6_02	17	16	24	7	22.60%
		Patser	V$ER_Q6_02	17	16	24	8	25.00%
		LMM	V$ER_Q6	15	16	15	0	0.00%
		ScanACE	M00959	8	16	11	1	n/a
GR	7	HMMER	M00921	7	7	10	2	16.70%
			T05076	7	7	7	1	12.50%
		Match	V$GR_Q6_01	7	7	9	3	25.00%
		Patser	V$GR_Q6_01	7	7	9	7	43.70%
		LMM	V$GR_Q6	6	7	6	1	14.30%
		ScanACE	M00921	4	7	4	1	n/a
HNF-1	18	HMMER	M00790	18	18	19	0	0.00%
			T01211	18	18	18	0	0.00%
		Match	V$HNF1_Q6	18	18	22	3	12.00%
		Patser	V$HNF1_Q6	18	18	29	1	3.30%
		LMM	V$HNF1_01	16	18	16	0	0.00%
		ScanACE	M00790	11	18	11	0	n/a
HNF-3	10	HMMER	M00724	10	10	10	1	9.10%
			T01049	10	10	10	2	16.70%
		Match	V$HNF3ALPHA_Q6	10	10	12	4	25.00%
		Patser	V$HNF3ALPHA_Q6	10	10	10	1	9.10%
		LMM	V$HNF3ALPHA_Q6	9	10	9	4	30.80%
		ScanACE	M00724	8	10	8	0	0.00%
HNF-4	10	HMMER	M00638	9	9	9	2	18.20%
			T00372	10	9	9	0	0.00%
		Match	V$HNF4ALPHA_Q6	9	9	9	2	18.20%
		Patser	V$HNF4ALPHA_Q6	10	9	9	2	18.20%
		LMM	V$HNF4ALPHA_Q6	7	9	7	0	0.00%
		ScanACE	M00638	3	9	3	0	n/a

The "Sites" column contains the number of sequences containing experimentally validated binding sites provided as input. "Target" represents the number of binding sites to be retrieved by a method to be considered successful, and "Distinct sequences identified" is the number of distinct sequences in which at least one true positive was detected. Because of partially overlapping hits, the actual number of true positives reported may be higher than the true number of sites. Not all matrices tested were available in the LMM matrix library; for those cases, the results obtained using the closest available LMM matrix are displayed in italics.

ISSN: 1471-2105