Table 3

Calculation of true and false positive and false negative rates from search results.

Score cut-off¹

BESs with positions

BESs in tail-to-tail BACs

BESs predicted to be in tail-to-tail BACs²

fp rate³

fn rate⁴

8

292,916

130,358

230,616

0.43

0.21

40

283,315

130,236

215,746

0.40

0.24

45

263,060

129,806

186,000

0.30

0.30

50

245,983

128,826

162,636

0.21

0.34

55

236,647

126,698

150,524

0.16

0.36

60

231,047

125,670

143,484

0.12

0.38

65

225,201

123,140

136,314

0.10

0.40

70

221,398

121,134

131,750

0.08

0.40

100

200,409

106,368

107,954

0.01

0.46

¹results from the MegaBLAST search on full length BESs using a contiguous word size of 8 the default score cut-off is 8, the results in this row correspond to the case where no score cut-off is specified.

²for each score cut-off the number of BESs predicted to be in tail-to-tail BACs assuming all BESs were correctly positioned.

³false positive rate

⁴false negative rate

Ratnakumar et al. BMC Genomics 2010 11:458   doi:10.1186/1471-2164-11-458