Table 2

Performance of different scores in recognizing functional and nonfunctional sites

Percent of binding sites assigned a lower p-value

Gal4p

Rpn4p

Positives (n = 10)

Negatives (n = 10)

Positives (n = 30)

Negatives (n = 29)

Halpern-Bruno vs simple

90%

30%

80%

25%

Halpern-Bruno vs S. cerevisiae alone

100%

40%

87%

34%

Simple vs S. cerevisiae alone

100%

30%

90%

48%

The score based on the Halpern-Bruno (HB) model assigns lower p-values to functional binding sites and higher p-values to nonfunctional binding sites than the simple score, defined as the average of the single species scores in at that position in the alignment. Both methods are far superior to p-values from S. cerevisiae alone. See text for details.

Moses et al. Genome Biology 2004 5:R98   doi:10.1186/gb-2004-5-12-r98