Figure 6.

RAG tree and dual graphs. (a) The library of topologies of RAG tree graphs between 2 and 10 vertices, with the second smallest Laplacian eigenvalues (λ₂) listed. (b) RAG dual graphs between 2 and 4 vertices, with topological classification (tree, bridge, and pseudoknot). The status of existing, RNA-like, and non-RNA-like topologies is represented by red, blue, and black (dashed), respectively (see text). The motifs in the yellow box indicate the five candidate motifs (C1, C2, C3, C4, and C7) as of 2004 [43] which have been identified as CPEB3, purine riboswitch, tRNA-like, Tombusvirus 3′ UTR region, and Flavivirus, respectively, in the updated RAG as of 2011 [37].