Figure 1.

Schematic of MultiFinder design. The sequence and support files are input files (aqua boxes) required by the sequence extraction script SequenceExtractor.pl to generate a number of input files (gray boxes) required by the motif finders gray MDscan, BioProspector, MEME, and AlignACE (green boxes). Statistics are generated for the motifs, similar motifs are merged and TRANSFAC IDs are assigned (tan boxes). Motifs from the previous step are combined and similar motifs are merged (purple box). Graphical output of the combined results (purple box) from all four motif finders is generated for each scoring function (red box).