RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology
Figure 1
RNA-As-Graph (RAG) tree representation of RNA secondary structures and graph partitions using the second Laplacian eigenvector.
(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.