Figure 4

Ambiscript Mosaic characters can be used to visually encode the degree of genetic variation present in aligned sequence motifs. Aligned sequences of the common bacterial HssRS DNA binding motif[11] are rendered individually with the black and grey-scaled consensus sequences at the bottom (A). Mosaic consensus symbols are not normally rendered with black-only symbols. The black consensus line shows the limited usefulness of black-only symbols in contrast with the grey shaded symbols in the grey consensus line. Unlike the grey shaded symbols, the black-only symbols are limited to indicating that one or more occurrences of the particular nucleotide can be found in that location, without communicating any sense of the percentage of occurrences. Because Ambiscript Mosaic consensus sequences are more compact than Sequence Logo graphs, they can be displayed using a progressive alignment in which polymorphisms are accumulated as you move down the list, much as numbers are tallied in a financial ledger (B). In both examples, the individual symbols that comprise the compound characters are shaded according to the likelihood of finding them in that particular position of the alignment. The distribution of Ambiscript characters above and below the centerline makes it easy to recognize the uninverted repeat in the aligned motif (bracketed between the grey bars).