Structural entropy plot for the HIV-1 genome (GenBank AF033819.3).

<p>UsingRNAentropy, the structural entropy was computed for each 100 nt portion of the HIV-1 genome, by increments of 10 nt; i.e. for 100 nt windows starting at genome position 1, 11, 21, etc. To smooth the curve, moving averages were computed over five successive windows. <i>(A)</i> Dotted-line displays moving average values of structural entropy; solid curve displays entropy Z-scores, defined by <math><mrow><mi>x</mi><mo>-</mo><mi>μ</mi></mrow><mi>σ</mi></math>, where <i>x</i> represents the (moving window average) entropy at a genomic position, and <i>μ</i> [resp. <i>σ</i>] represents the mean [resp. standard deviation] of the entropy for 100 nt windows. Some of the lowest entropy Z-scores are -2.69 at position 4060, -2.46 at position 8700, -1.95 at position 4040. <i>(B)</i> NCBI graphics display of the HIV-1 genome, for comparison purposes. Low entropy (negative Z-score) regions do not appear to correspond with the start/stop location for annotated genes. In data not shown, we also computed <i>positional entropy</i> values [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137859#pone.0137859.ref021" target="_blank">21</a>] for the same windows, and determined a Pearson correlation of 0.7025 [resp. Spearman correlation of 0.6829] between (moving window average) values of entropy and positional entropy.