Hi:
We know that ancestral repeats have long been used as neutral evolving
sites, when deciding the evolution situation of non-coding regions. but I
am considering how to calculate the substitution rate of ARs. For example,
if I want to decide the evolution situation of rRNA genes in human, mouse
dog horse and cat, I can choose ARs in those species as neutral sites. Now
I get the ARs in those species(by DataRepeat), but I don't know how to
calculate the substitution rates.
I read many papers that usually describe the method briefly, authors said
that they "regional nucleotide substitution rate in ancestral repeat sites,
tAR, was calculated separately for each 5-Mb window by maximum likelihood
estimation of the parameters of the REV model using only the ancestral
repeat sites in the window (average of about 280,000 sites per
window)"[Initial sequencing and comparative analysis of the mouse genome].
But for multi-way aligning ,there should be many sites different in the
same window. And there are many types of ARs, how could I merge them
together in windows?
thanks
Richard Wang
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