New base-base interaction predictions. For each numbered and asterisked prediction in Figure 5 the statistical significance (p value) of the mutual information between the two alignment columns is shown, followed by the relative frequencies with which specific combinations of bases are observed in those columns. Base pair geometries and isostericity groups compatible with the asterisked pairs are described in more detail elsewhere . These descriptions include the relative orientations of the glycosidic bonds across the pair (cis or trans), the edges of each base that interact (WC, Watson-Crick; H, Hoogsteen; SE, sugar edge; bifurcated, intermediate between two edges), and the relative backbone strand geometry (parallel or anti-parallel) assuming both glycosidic bonds are in default anti conformations.
Barrick and Breaker Genome Biology 2007 8:R239 doi:10.1186/gb-2007-8-11-r239