Extensions to the graph kernel for GraphProt . (A) Transformation of a hypergraph to an equivalent incident graph. (B) Mixed abstract–ground level hypergraph features. Two identical occurrences of the subsequence UUC yield two independent features, one that is aware of the internal loop location and the other that is aware of the hairpin loop location. (C) Undirected to directed graph transformation: edges are directed following the 5′ to 3′ direction. An additional copy of the graph with inverted edges and relabeled vertices (using the prefix r) is added. (1) A fragment C(G-C)U is highlighted. In the undirected case, the reversed substructure U(G-C)C generates identical features. (2) The directed treatment creates features that can be used to discriminate between the two fragments. The neighborhood of vertex G generates the feature (G-C)U in the main direction and (r G-rC)rU in the reverse direction. (D) Viewpoint extension: a large window allows the RNA molecule to fold correctly; however, as we are interested in a local phenomenon, we restrict the extraction of features to a smaller subportion that reflects the relevant part of the RNA, that is the RBP binding site. We highlighted the viewpoint area in yellow. We highlighted in red the portion of the folded RNA molecule that will be accessed to extract features when the parameters for the NSPD Kernel are radius + distance = 5. RBP, RNA-binding protein.