Frequency/distribution of nucleotides/amino acids before selection

[Dr.Ram Samudrala]

fatherdes at hotmail.com wrote:

>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).

Do you know of a reference that gives these numbers for all the
variables you mention above?  I found a few Bernardi references, but
the ones I saw had to do with analysis in the degenerate position of
codons (which is also an interesting way of getting the frequencies I
want).  I was not able to find one that gave frequencies for introns
or other non-coding regions.

I wouldn't mind repeating this, and with the wealth of data out there,
it should be easily possible.  However, what I have also been unable
to find is a database of non-redundant gene sequences.  It seems to me
such a database would be necessary to do a proper analysis, as
multiple copies of a single gene would bias the nucleotide
frequencies.

Thanks for your response; I appreciate it!

--Ram

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