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Figure 2 | BMC Research Notes

Figure 2

From: SigWinR; the SigWin-detector updated and ported to R

Figure 2

SigWinR rectangular Ridgeogram of the gene density in the circular bacterial genome of Staphylococcus aureus. The SigWinR rectangular Ridgeogram showing the significant windows of gene density, i.e. the number of nucleotides that belong to a gene, on the DNA positive strand of the circular genome of bacterium Staphylococcus aureus using a bin-size of 1 kb. The input values are calculated per 1 kb bin as the difference of the number of gene nucleotides between the top strand and the bottom strand divided by 1,000. The DNA origin-of-replication (ori) and replication terminus (ter) are at position 0 and ~1,500 at the X-axis, respectively. The Y-axis shows the window size. The known, skewed gene distribution with over-representation in the DNA replication leading strand (ori → ter) and under-representation in the lagging strand (ter → ori) [5, 6], are clearly visible and most pronounced at a window size of half the total sequence length. Furthermore, the Ridgeogram shows that on the leading strand near the ter, the gene density is highest. The dotted triangle is placed in this figure to illustrate which part of this rectangular Ridgeogram represents the content of the common (triangular) Ridgeogram. Below the Ridgeogram, a XY-plot of the 1 kb bin gene-density values of the whole genome sequence is depicted.

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