Figure 3.

Significance of binding sites in pairwise or three-way comparisons at similar evolutionary distance. (a) Histogram of the percent identities of all aligned noncoding regions of S. cerevisiae and S. kudriavzevii (open squares) and S. cerevisiae, S. paradoxus and S. mikatae (filled squares). (b) Median p-values of functional matches (positive set, gray bars) and the nonfunctional matches (negative set, open bars) for S. cerevisiae and S. kudriavzevii alignments (left) and S. cerevisiae, S. paradoxus and S. mikatae alignments (right). The similarity of these p-values supports the idea that multiple similar genomes can be used to span longer evolutionary distances, but at these close evolutionary distances provide little additional power.

Moses et al. Genome Biology 2004 5:R98   doi:10.1186/gb-2004-5-12-r98
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