Table 1.

Performance of the hill climbing algorithm on well-characterized S. cerevisiae regulons. The reported binding sites were each run through the hill climbing algorithm to determine the algorithm's ability to generate a representative consensus motif given only one instantiation. Abbreviations are as follows: |B|-the number of genes in the regulon; HC(b)-the consensus motif reported by HC(·) that had the highest Φ score; ΔSig-the maximum change in Sig score due to HC for any binding site; Φ b-the maximum Φ score for any one binding site; Φ HC-the Φ score after HC is run on the known binding sites.

Regulon	|B|	HC(b)	ΔSig	Φ b	Φ HC
BAS1	13	gagtca	17.80	0.36	0.36
CPF1	3	cwcgtgrm	17.26	0.61	0.55
CSRE	6	tcmwttcayccg	28.33	0.27	0.29
GATA	5	gatwas	40.66	0.73	0.56
GCN4	20	bagtcab	26.10	0.29	0.44
GCR1	9	ctyhc	12.59	0.43	0.18
GLN3	3	ytaatctaatc	10.28	0.63	0.64
HAP2	5	gttggttggtgga	13.37	0.37	0.23
MATA1	3	sactaattaggaaa	10.00	0.33	0.36
MATA2	12	brdgtaadt	29.17	0.21	0.48
MCM1	43	chnwttmggdaa	53.31	0.05	0.29
MCB	4	wcgcg	40.46	0.62	0.78
MIG1	13	ccccrbwww	19.43	0.21	0.38
PDR3	10	hyccrcggr	138.96	0.50	0.71
PHO2	6	gtaaattagttaatt	0.00	0.40	0.21
PHO4	12	cacgtggracta	8.41	0.13	0.14
RAP1	18	acacccagacmkc	12.98	0.09	0.15
REB1	20	bvywacccs	25.01	0.36	0.47
ROX1	8	ycyattgttctc	14.86	0.13	0.38
RPA	3	tctcggcggtta	0.00	0.34	0.34
SCB	8	cdcgawa	37.79	0.58	0.72
SFF	4	aggtmaacaa	5.85	0.25	0.50
STE12	6	atgmaac	24.74	0.48	0.53
TBP	20	yatava	18.44	0.44	0.20
UASCAR	4	ttgccmttmgc	16.63	0.25	0.40
UASH	21	gwgtagtgaca	12.12	0.05	0.05
UASPHR	23	cgtggatgaaac	6.44	0.04	0.04
UIS	5	aaaatagcgcctc	0.00	0.22	0.20
URS1H	12	wdwtwgccsccvw	61.10	0.15	0.65
Average	11		24.21	0.33	0.39