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Figure 4 | BMC Genomics

Figure 4

From: Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions

Figure 4

Symmetric map (biplot) of trinucleotides and genomic fragments from a Factorial Correspondence Analysis (CA). Correspondence analysis was performed as described in Methods. The 1st and 2nd coordinates plotted in the map represent 65% of the total inertia. Data points that are close to the origin (0,0) have no compositional bias (homogeneous usage) while points that move away from the origin represent larger deviations. In the plot, data points corresponding to genomic fragments (N = 40 Kb) are shown in green, and are overlayed with data points corresponding to centromeric sequences in blue), data points corresponding to TgTAS-like sequences (in black), along with the 64 trinucleotides (in magenta). Opacity of colours is related to how well each point (its inertia) is represented in this 2 dimensional subspace. Plot interpretation: fragments (dots) that are close in the plot have similar trinucleotide composition, and trinucleotides (triangles) which are close to each other frequently appear in the same fragments. Distances between dots and triangles have no meaning, however, the directions of dots and triangles from the origin (0,0) are meaningful (e.g. fragments on the right of the origin use more TAA, CTA, ATT (and their reverse complements TTA, TAG, AAT) and less AGA, CTC and CGC (and reverse complements TCT, GAG and GCG), whereas the opposite is true for the fragments lying on the left of the origin).

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