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Fig. 3 | Genome Biology

Fig. 3

From: High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life

Fig. 3

Two summaries of the ∆LFE profiles demonstrate the consistency and diversity found. a Characteristic ∆LFE profiles for species belonging to different taxons. The format of the plots appears in the upper left corner: ∆LFE bias is shown (by color) for windows starting in the range 0–150 nt relative to the CDS start, on the left, and CDS end, on the right; red denotes negative ∆LFE (stronger-than-expected folding) while blue denotes positive ∆LFE (weaker-than-expected folding; see the scale at the upper-right corner). The characteristic profiles for each taxon were calculated using clustering analysis, by grouping similar species according to the correlation between their profiles (see “Visualization” under the “Methods” section for details). The bars (in turquoise) appearing to the right of each characteristic profile indicate the relative number of species it represents. The full ∆LFE profiles for all species appear in Additional file 1: Figure S7. b. Summary of ∆LFE profile diversity for all species using dimensionality reduction to 2 dimensions with PCA (see explanations about PCA in the main text), with similar values (profiles) mapped to nearby positions. Background shading (blue) indicates density (see “Visualization” under the “Methods” section for details). This shows most species have similar profiles (located near the center), but different kinds of less typical profiles are also represented. Top, CDS start; bottom, CDS end. Short species names are listed in Additional file 1: Table S3

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