RankVISTA conservation plots depict evolutionarily conserved segments in pairwise or multiple alignments as a bar graph, where the heights scale with statistical significance [-log10(P-value)]. For example, a height of 4 indicates that the probability of seeing that level of conservation by chance in a neutrally-evolving 10-kb segment of the base sequence is less than 10-4.
RankVISTA graphs are based on the Gumby algorithm, which estimates neutral evolutionary rates from non-exonic regions in the multiple sequence alignment, and then identifies local segments of any length in the alignment that evolve more slowly than the background. The phylogenetically weighted log-odds conservation scores of conserved segments are translated into P-values using karlin-altschul statistics. Gumby has no window-size parameter, and no fixed percent-identity threshold either. Since the algorithm uses a more-conserved-than background paradigm, it can perform phylogenetic shadowing (close species) and footprinting (distant species) with equal facility.
NOTE: Since the input alignment is its own training set, small or grossly incomplete alignments are to be avoided:
RankVista regions are colored according to their annotation, as seen in the figure above. Note that RankVista coloring is based on exon annotations of all aligned sequences, not just the one currently used as the base. Consequently, an unannotated region in the base sequence might still be colored as an exon because of annotations from other sequences. In another deviation from the standard scheme, RankVISTA colors UTRs and coding exons the same, since they are treated identically by Gumby.
Martin J, et al. The sequence and analysis of duplication-rich human chromosome 16. Nature. 2004 Dec 23;432(7020):988-94.