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On coverage, domains and function

Posted by J_Fay on 04 Jan 2007 at 16:10 GMT

I have a few comments.
1. The data have been available for some time, and now finally, a paper on gain and loss of genes in primates. Now that there is a list, how does one figure out the functional significance of each event, if any? I think this will be a real challenge. Dietrich gave a seminar here at WashU and one of his main points is that he has found multiple QTL for innate immunity in mouse map to duplicated regions of the genome.
2. If you look at a cartoon of any well characterized protein family, most people note differences in the presence and absence of domains to distinguish family members. It would be nice to see the work extended to gain/loss of domains or exons.
3. Is there any way to incorporate genome coverage into the evolutionary model. In other words, the absence of a gene on the tips of a tree is not known but is a probability that depends on genome coverage.