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.

Marinescu et al. BMC Bioinformatics 2005 6:79   doi:10.1186/1471-2105-6-79