Pairwise comparative map is designed to replace an earlier mapping component called CPG Map that was written by the same programmer. A number of functionality problems existed with CPG Map so it was decided to rewrite an improved version of the component. Both maps are designed for showing the similarities or differences between genetic maps by drawing lines between homologous loci on the maps but differ in the style in which they do so.

A CPG Map (image available) consists of a hierarchical collection of maps with lines drawn between the maps at the lowest level of the hierarchy. For example, you could draw both a physical and a linkage map for Arabidopsis and Brassicas chromosome IV on the same page, (i.e. four maps on the page). Lines would link the homologous loci on the Arabidopsis linkage and physical maps and similarly lines would link the homologous loci on the two Brassicas maps. The homology between the two sets of double maps was shown by the use of colour- as the user moved the mouse over a locus, all homologous loci in all the maps on the page would be highlighted.

It became apparent that the use of colour alone did not sufficiently highlight these homologies- lines were needed between all the homologous loci on all the maps. The only problem was that if more that two maps were drawn, the jumble of lines looked like spaghetti! It was decided to break down the collection of maps in to pairwise comparisons. For example, the image below shows a CPG Map of two Arabidopsis Maps and two Brassicas maps. To represent this as a pairwise maps, you would have to draw six PCM units.

The higher level PCM component, Multi PCM allows you to draw a number of maps together like in the above diagram.

Although the new version of the map comparison tool requires you to draw a lot more maps to cover the same data, the information that one picks up visually far exceeds that of CPG Map as lines are drawn  between all the maps.

ŠJeremy Dickson, October 1998.