Table 3

Sensitivities and positive predictive values (PPVs) of HexDiff and other algorithms. A known CRM was considered recovered if a predicted CRM overlapped it by at least 50 bp. The PPVs in this table are italicized because they are estimates of the true PPVs. Without complete knowledge of all CRMs that are present in the 16 sequences, it is possible that some of the predicted CRMs that are labeled as false positives are actually true positives.

Algorithm

CRMs Recovered

Num CRMs

Sensitivity TP/(TP + FN)

True Positives

CRMs Predicted

PPV TP/(TP + FP)


HexDiff

36

52

69.23%

35

104

33.65%

Ahab

23

52

44.23%

20

35

57.14%

Cluster Buster

31

52

59.62%

23

88

26.14%

MSCAN

34

52

65.38%

42

226

18.58%

MCAST

43

52

82.69%

53

499

10.62%

LWF

27

52

51.92%

48

433

11.09%


Chan and Kibler BMC Bioinformatics 2005 6:262   doi:10.1186/1471-2105-6-262

Open Data