Fig. 2
From: Subtype classification and functional annotation of L1Md retrotransposon promoters
Application of profile-HMM helps identify monomer subtypes and common truncation sites. a Visualization by tSNE of subtype identification based on the first 100 principal components using the HDBSCAN algorithm followed by k-NN clustering. b Heatmap showing sequence variation measured by edit distance for both intra- and inter-group subtypes of the Type A monomers. c – e Truncation profile indicated by the posterior expected number of states (top), and weighted read pileup of CAGE-seq data (bottom). Antisense read pileups were visualized as negative values