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. 2014 Sep 4;9(9):e106074. doi: 10.1371/journal.pone.0106074

Figure 1. RNA-As-Graph (RAG) tree representation of RNA secondary structures and graph partitions using the second Laplacian eigenvector.

Figure 1

(A) Examples of RNA secondary structures, their corresponding RAG tree graphs, Laplacian matrices, and the second eigenvectors: (a) signal recognition particle (PDB code: 2XXA, Graph ID: 6_1); (b) glycine riboswitch (PDB code: 3OWZ, Graph ID: 6_2); (c) RNase P (PDB code: 3Q1Q, Graph ID: 6_5). (B) Graph partitioning using the cut values of the median, sign, or the largest gap of the second Laplacian eigenvector with examples of three RAG graphs 6_1, 6_2, and 6_5.