Table 2

Performance metrics for genome scans

Execution time (hrs) *

Number of sites found^

Site

Length

Weight matrix version

Num. sites in Model

R_i,min

R_seq

Mosix

Scyld

R_i≥R_i,min

R_i≥R_Seq

Unique Promoters with R_i≥R_seq

Promoters with multiple sites (%) R_i≥R_seq

PXR

23

1

15

7.1

17.1

6.5

4.3

3.48e5

218

200

8.3

PXR

23

2

19

7.1

17.0

6

3.5

4.97e5

391

365

6.6

PXR

23

3

32

7.1

14.9

7.1

4

1.10e6

3393

3036

10.5

PXR

23

4

48

7.1

14.4

6.8

3.8

1.44e6

7694

6439

16.3

NF-κB

10

3

75

2.6

10.9

5.8

-

1.16e7

74050

33340

54.9

AHR

17

1

30

2.8

9.4

6.3

-

1.20e7

42487

24764

41.7

Acc

28

12

1.08e5

2.4

7.4

14.5

-

4.87e7

-

-

-

Don

7

5

1.11e5

2.4

6.7

10.5

-

4.85e7

-

-

-

SC35

8

1

30

0.4

3.6

19

-

1.07e8

-

-

-

Abbreviations. Site: Binding site information matrix; PXR: PXR/RXRα; NF-κB: NF-κB p50/p65 subunits; Acc: Splice Acceptor; Don: Splice Donor; Length: Length of the site in nucleotides; R_i,min : R_i,minimum (in bits); R_Seq : R_sequence (in bits) * total runtime for both scan and promotsite programs ^Results of information analysis with the PXR/RXRα, NF-kB and AHR matrices of promoter regions (10 kb upstream of transcription initiation site) for all transcripts mapped in reference genome sequence. Complete gene sequences (from the transcription initiation site to the terminal sequence of the 3' UTR) were analyzed with the Acc, Don and SC35 matrices.

Gadiraju et al. BMC Bioinformatics 2003 4:38   doi:10.1186/1471-2105-4-38