Sure, here's some more info on it. A variety of different factors have been shown to display chromosomal dependencies in the last few years. For instance, there is a profound chromosomal dependence of gene-expression, a strong tendency towards co-expression of neighbouring genes, chromosome-wide patterns in mutation rates (SNPs), and of course in GC content (e.g. isochores).

There are a variety of different ways to slice these things up statistically and experimentally, but it seems to me that the most evident display technique for any of these is just to show a chromosome, along with some colour coding to indicates regions where this phenomenon occur together, or... don't. You can imagine a figure showing the 20+ chromosomes with their particular data sets....

So, the underlying colour coding will be variable. My first pass attempt is just to colour according to cytogenic bands. So, just as that link I gave showed a physical chromosome (that's Rat-1, I think), I would show that. Then, as a first attempt I would colour different bands differently according to, say, how many SNPs they had in them.

It would be a highly intuitive display technique for all biologists, and if I can code it reasonably well, it should be flexible enough to be extended easily to any data set.

I don't believe there is anything in BioPerl to deal with chromosomes, but I'll post to that list and see what they say.

Thanks for the interest!