Distribution of Cys₂-His₂ zinc fingers in genes within D. melanogaster genome. (A) Distribution of the number of fingers identified within each zinc-finger-containing gene in the fruit fly genome. (B) A schematic depicting canonical DNA recognition by a Cys₂-His₂ zinc finger. The numbered spheres on the α-helix represent the residues that are anticipated to contact DNA in the canonical recognition mode. These residues are numbered relative to the start of the α-helix and make contact (arrows) with their respective color-coded DNA bases (boxes). Each finger (in an N-terminal to C-terminal orientation) binds its DNA subsite (labeled 5′ to 3′) in an anti-parallel arrangement. (C) Number of ZFPs attempted and the success rate of these B1H selections. (D) Comparative MatAlign analysis of ZFP motifs determined by B1H and other methods (Hallikas et al. 2006; Robasky and Bulyk 2011). B1H motifs are designated by red ovals.