In the last section, two CPG Map examples were given; the first showing double maps and the second showing single maps. However, these did not demonstrate the main feature of CPG Map: The comparative mapping part of it. CPG Map was just acting as a map viewer in these cases. However it is possible to set up reasonably complicated relationships between the different loci on the maps.
If you examine the real CPG Maps from which the images in the introduction are derived, you find that as you pass the mouse over a locus (or click on one), it highlights. If comparative mapping data is being displayed, as you highlight a locus, all other homologous loci in all of the double or single maps get highlighted. It is this function that makes it useful as a comparative mapping tool.
So for example, if you had the data, you could set up a CPG Map to show four double maps: The physical and linkage maps of human chromosome IV, mouse chromosome IV, chimpanzee chromosome IV and pig chromosome IV. As you passed the mouse over any locus in any double map, all loci that had been mapped in the other species would be highlighted.
Another type of relationship called ownership is also available. This is similar to the homology relationship but is only one way. Both relationships are discussed in more detail later.