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Frequency/distribution of nucleotides/amino acids before selection

fatherdes at hotmail.com fatherdes at hotmail.com
Thu Oct 22 10:15:36 EST 1998

In article <70l72a$b03 at net.bio.net>,
  expt at alanine.ram.org wrote:
> Have there been any estimates published on the frequency/distribution
> of nucleotides/amino acids in DNA/protein sequences PRIOR to
> selection, i.e., before selection kicks in? I can get the frequencies
> of amino acids in known protein sequences, but these proteins have
> generally arisen through natural selection.
> --Ram

There has been quite a lot of work done on comparing nucleotide frequencies in
different parts of the genomes of different organisms (e.g. numerous papers by
Giorgio Bernardi and co workers).  here the frequency seen in introns, gaps
between genes and pseudogenes will be close to what you need but it varies
strongly with organism and even within genomes.

I do not know how one would estimate a comparable set of figures for amino
acids.  You could make guesses based on an expected frequency of amino acids
from the expected frequencies of the 64 different codons, given the nucleotide
frequencies but I do not know how to do that exactly and such calculations are
fraught with complications.

Des Higgins
Biochemistry Dept.
University College

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