Fig. 5
From: DotAligner: identification and clustering of RNA structure motifs
De novo homologous RNA motif identification. a,b Reachability plots of OPTICS clustering display the OPTICS-derived ordering of points (x-axis) and their distance to the nearest neighbour (y-axis). Colours represent significant clusters. a Clustering of Rfam benchmarking data indicating the distance to the nearest neighbour. b Clustering of 2650 ENCODE eCLIP peaks + 100 Rfam controls that overlap evolutionarily conserved secondary structure predictions. The dominant RNA binding protein in each cluster is displayed next to significant clusters. Those with an asterisk are portrayed below. c Multiple structure alignment generated by mLocaRNA on the sequences from a cluster containing both Rfam SNORNA72 sequences and DKC1 (a snoRNA-binding protein) eCLIP peaks. An unannotated DKC1-bound sequence is marked with an asterisk. d–f RNAalifold-predicted consensus RNA secondary structures: d Structure of the alignment displayed in (c). e Structure of a cluster of impartially detected DKC1-bound snoRNAs. f Structure of a novel UPF1-bound motif. dist. distance