The optional graphical representation of results mimics a hand analysis of the alignment using coloured marker pens. In Figure 3 the alignment is shown divided into three sub-families. Within the sub-families, at each alignment position, the amino acids are appropriately highlighted. Conserved sub-groups, sub-groups showing identity and positions that show identity across the whole alignment are labelled. Figures 5a and 6 illustrate the graphical representation applied to the annexin and SH2-domains.
Three highlighting methods have been explored. Monochrome methods allow grey shading (Figures 5 and 6) or the use of different fonts (not shown) to highlight the differences in conservation. Grey shading is preferable for publication whilst unshaded alignments are useful as working copies for hand annotation. Colour may be specified as an alternative to shading to provide additional visual impact.