Hello, Richard. Unfortunately your question is beyond the scope of this mailing list as we do not provide advice regarding scientific direction, but focus on browser usage issues.
Please contact us again at [email protected] if you have any further browser-related questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of meng wang Sent: Tuesday, February 28, 2012 11:54 PM To: [email protected] Subject: [Genome] How to calculate the substitution rate of ancestral repeats 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
