Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

Table 2 Combination of motif discovery programs based on measures of true positive and false positive nucleotides

Tools	Synthetic data (AM)		Semi-synthetic data (AR)		Real data (MR)		Averages
	nTP	nFP	nTP	nFP	nTP	nFP	Average nTP	Average nFP
Bioprospector	995	10668	940	9889	1638	11797	1191	10785
MEME	1503	21861	1134	25832	798	42253	1145	29982
Weeder	2104	86064	2251	74945	1895	53365	2083	99561
Combined	3067	110825	2876	102531	3462	110089	3135	107815
Combined filt.	2813	85186	2676	73534	3078	81756	2856	80159

The Table shows the numbers illustrated in Figure 3A-C. Each value is the average result of three runs for each standalone unfiltered program, as well as the scores after combining the outputs of the three programs without filtering (combined) or with filtering (combined filt).

ISSN: 1471-2229