Saturday, January 12, 2008

Missing information regarding mutation rates

I am interested in using your results about substitution rates you published in the paper: "Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes"
I need to use your results for my research however, there are some missing information in your paper specifically in Figure2-A the following mutation rates are missing:

  • G-> C with neighboring of C

  • G->T with neighboring of C

  • G->A with neighboring of C

Another point is that Dinucleotide effect rates are done in CpG rich or poor or general areas also is it possible you send me a table of these numbers so I get them more accurate than extracting them from that graph.

We excluded CpG di-nucleotides from our analysis since they are known to have hyper mutation rates than any other di-nucleotides, due to the mechanism of methylation–deamination of cytosine. In fact mammalian genomes are depleted of CpGs, except of CG islands.

We also mentioned this in the paper.


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