Figure 3.

UCR clusters arose independently during evolution.A and B. The 5-mer composition of UCRs and 50 bp-flanking sequences were taken as input for the Minimum Curvilinear Embedding analysis and the top three dimensions are depicted here. Clusters and species are marked with different colors as indicated in the inset on the lower right corner. C. UCR cluster relationships. Each node represents a UCR with flanking sequence. The similarity between nodes in a same cluster is omitted to avoid extreme density. A cluster centroid is made instead and connected to the components to show membership within the cluster (purple lines). The gray lines show sequence similarities between nodes in different clusters. Clusters with fewer than 7 nodes are not shown. UCRs from sea anemone predominate in this figure due to the large number (3,807 among all 4,817 UCRs).

Ryu et al. BMC Evolutionary Biology 2012 12:236   doi:10.1186/1471-2148-12-236
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