Syntenic dotplot
Syntenic dotplots are a type of scatter-plot. Each axis represents a sequence laid end-to-end, and each dot in the scatter-plot represents a putative homologous match between the two sequences. Often, these dotplots are used for whole genome comparisons within the same genome or across two genomes from different taxa in order to identify synteny. Synteny is defined as two or more genomic regions that are derived from a common ancestral genomic region. The evidence for synteny is the identification of a set of homologous genes in two genome that have a collinear arrangement. When such a pattern of gene-order conservation is discovered, the most parsimonious explanation is that the two regions are related through a common ancestor. While syntenic dotplots are useful for identifying related genomic regions, they are also useful for identifying genomic regions that have undergone an evolutionary change in one of the two genomes being compared. For example, insertions, deletions, duplications, and inversions are readily identifiable from these plots.
