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Figure 2 | Microbial Informatics and Experimentation

Figure 2

From: PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences

Figure 2

Periodicity scan of the H. influenzae chromosome. a) The main periodicity scan plot. The level of grey signifies the intensity of the periodic signal for the chromosomal location shown on the horizontal axis and the period shown on the vertical axis. The periodicity was evaluated in a 10 kb window was shifted by 5 kb at a time. The white areas correspond to the relative signal intensity Q*(P)≤1.8 whereas black shading indicates signal intensity Q*(P)≥4.0. The level of gray continuously changes from white to black between the values 1.8 and 4.0. b) The fraction of windows with the maximum signal at the period indicated by the abscissa plus or minus 0.2 bp, regardless of the height of the maximum. c) The fraction of windows with the signal intensity for the given period Q*(P)≥2.0 (cyan), ≥2.5 (magenta), ≥3.0 (blue), ≥4.0 (green), and ≥6.0 (red). See text for details. The definitions of indices MaxMax, PMaxMax, Max2, and PMax2 are demonstrated in panels b and c. The indices Max3 and PMax3 are analogous to Max2 and PMax2 but derived from the blue section of the plot.

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