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Table 2 Performance of different scores in recognizing functional and nonfunctional sites

From: MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model

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%
  1. 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.