Clustering of glycine riboswitch aptamers identified within the Bacilli class of bacteria.
A) Aptamers within the Bacilli bacterial class were identified and clustered based on RNAmountAlign pairwise similarity (visualized at threshold of 12). B) Sub-clusters (communities) were identified using the four community detection functions within R’s igraph package. Two communities were identified that contain two different aptamer types: aptamer-1 and singlet type-1, and aptamer-2 and singlet type-2 that regulate GCV and TP respectively. Network shows visualization of the community detection algorithm cluster_fast_greedy (as implemented by R). Node colors correspond to distinct clusters detected. C) The two sub-clusters containing different aptamer types were parsed from the overall network, the tandem aptamers’ partners were added to the set (as an out group within the same context), and graph clustering was visualized (RNAmountAlign threshold of 5). D) Edge density between aptamer groups was calculated for networks generated across a range of RNAmountAlign edge-weight thresholds. Dotted red line indicates the RNAmountAlign threshold (5) at which the networks in (C) were visualized.