Human/chimpanzee and human/mouse ApoE genomic-sequence comparisons. (a) PipMaker analysis with human sequence depicted on the horizontal axis and percentage similarity to chimpanzee on the vertical axis. Exons are indicated by black boxes and repetitive elements by triangles above the plot. Each PIP horizontal bar indicates regions of similarity based on the percent identity of each gap-free segment in the alignment. Once a gap (insertion or deletion) is found within the alignment, a new bar is created to display the adjacent correspondent gap-free segment. (b) VISTA analysis with human sequence shown on the x axis and percentage similarity to chimpanzee on the y axis. The graphical plot is based on sliding-window analysis of the underlying genomic alignment. In this illustration, a 100-bp window is used that slides at 40-bp nucleotide increments. Blue and pink shading indicate conserved coding and noncoding DNA, respectively. Green and yellow bars immediately above the VISTA plot correspond to various repetitive DNA elements. (c) PipMaker analysis with human sequence depicted on the horizontal axis and percentage similarity to mouse on the vertical axis. (d) VISTA analysis with human sequence shown on the x axis and percentage similarity to mouse on the y axis. Two experimentally defined enhancers are indicated on each of the plots (4–6).