Fig. 1.

Examples of RNA-RNA interactions structures. The primary interaction region(s) are highlighted in grey in the experimentally supported structural models from the literature: (A) ompA-MicA: (Udekwu et al., 2005); (B) sodB-RyhB: (Geissmann and Touati, 2004); (C) fhlA-OxyS: (Argaman and Altuvia, 2000). Hybridization probabilities computed by rip2 are annotated by black boxes for regions with a probability larger than 10%. In many cases, the computational predictions identify additional hybridization regions that may further stabilize the interaction.