The number of sites per intergenic region
The number of potential sites to consider in each intergenic region, and their respective weights, are additional parameters that can be set by the user to best capture the underlying biology in the system under study. Generally speaking, for i ≥ 1, the algorithm detects that an intergenic region with sites is significant when its ith best site is surprisingly strong given its rank as the ith best site. The weight wi should be chosen in proportion to the number of such intergenic regions that are expected to have i as the first/lowest rank that appears strong by this test. We have set the default to have weights (w1, w2) = (0.9, 0.1) under the assumption that approximately 90% of intergenic regions with sites will have a strong site; among the remaining intergenic regions with sites, nearly all will have a site that is surprisingly strong given its rank as second strongest. (See the Methods.)