Cumulative score distributions. a) The cumulative distribution of (a) Qacc, (b) Qsse, and (c) Qand = Qacc + Qsse scores calculated for true motif matches (true motifs), and for random matches (random matches) in non-wildcard positions. Red dashed lines indicate the percentile cut-off ensuring that the lower 40% random matches fall in the "sparse" bin. The consequent percentage of true motifs falling in the "sparse" bin is about 15% (accessibility) and 20% (secondary structure). This cut-off corresponds to Qacc~0.3 and Qsse~0.7. Black dotted lines indicate the percentile cut-off that guarantees that the enriched bin collects at least the top 30% true motifs. This cut-off corresponds to Qacc = 0.76, Qsse = 1.5, and Qand = 2.243.
Via et al. BMC Bioinformatics 2009 10:351 doi:10.1186/1471-2105-10-351