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

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.

ISSN: 1474-760X