Abstract
The numerous whole genome sequencing projects completed or underway makes it possible to conduct large-scale comparison within or between species. The common and highly successful approach to comparing large tracts of DNA is to conduct a dot-matrix pair-wise analysis. However, one of the major limitations of this approach is that it only compares pairs of sequences. In this paper, we describe a dot-matrix algorithm that is able to compare two or more sequences and identify conserved regions shared between those sequences. The display is still a two dimensional image with the axis corresponding to the first two input sequences and the conserved regions for all remaining sequences superimposed. It becomes immediately possible to interpret those regions that are evolutionary or functionally conserved between sequences. To demonstrate this approach, this tool is applied to wheat, barley, and rice related genome sequences and the results are discussed.