In article <3vs26l$4s3 at knot.queensu.ca> sibbald at qucis.queensu.ca (Peter Sibbald) writes:
>This means that
>i tallied up the frequencies of AA, AC, AG.... TT and compared them
>to the frequencies expected given the frequencies of the individual
>bases. You might expect if junk was junk that the frequencies are
>rather unconstrained (doublet that is) and that they would differ
>from those in the other categories. Not so. The frequencies in
>different categories are well correlated.
I'd be interested in why you reject the alternative hypothesis that the
doublet frequencies are controlled mainly by mutational processes (which
are the same across the genome). For example, a particular doublet
might mutate more often due to some physical mechanism, and thus its
steady-state frequency would be lower.
I would think that if "junk" DNA has a structural role, it would be
expected to have different doublet frequencies than coding and
regulatory DNA, not the same ones.
Mary Kuhner mkkuhner at genetics.washington.edu