Introduction

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Pairwise Comparative Map (PCM) is a Java bioWidget (or programming component) that shows two genetic maps of any type and species adjacent to each other and draws lines between the homologous loci on each map. One can resize the length of each map, invert each map, and swap the maps on either side.

An image of an example PCM is shown below:

pairwise1.gif (20238 bytes)

	In this case an Arabidopsis physical map is being compared to an Arabidopsis linkage map. The title of the map and it's units are shown at the top and the green bar in each case represents the length of the chromosome, (or whatever portion of it is being shown). The adjacent scale bars indicate the general loci positions.
	Loci that are present in both maps are linked by a connecting line. It is possible for a locus to exist on one map without being mapped to a homologous locus on the other map. It is also possible for a locus on one map to link to more than one locus on the other map- multiple lines from that locus are seen.
	One can also show a map on its own without showing one on the other side like in the given image. Obviously no connecting lines are drawn.

Multi PCM

A higher-level component called Multi PCM exists in which a number of PCMs are placed in a scrollpane, (see image). Highlighting a locus in one PCM has the effect of highlighting all the homologues across all of the PCMs. The maps are colour coordinated across the Multi PCM to unify the maps originating from the same database.

ŠJeremy Dickson, October 1998.