Human codon bias

PJOB obrien at pharm.med.upenn.edu
Thu Nov 17 10:51:33 EST 1994


In article <obrien-161194114205 at brass2.med.upenn.edu>,
obrien at pharm.med.upenn.edu (PJOB) wrote:

> Hi,
> 	I'm looking for a reference or online source that can tell me the codons
> preferred in human genes.  I'm trying to make a degenerate oligos for PCR
> of a member of a protein family, and there are too many permutations in my
> current scheme.  Would it be a valid strategy to reduce this number by
> leaning towards preferred codons?  Thanks in advance...
 
I.  FYI: I was given references (thanks to the donors)

Wada et. al. NAR 18(suppl.):2367, 1990
R. Lathe  J. Mol. Biol. 183:1-12, 1985  

Unfortunately, in the 11 amino acid sequence for which I am making a
degenerate oligo, the wild type protein uses the "most likely" codon in
only three positions, each of which have only two possible codons anyway. 
It would seem that my protein is a nonconformist...  This emphasizes the
second part of my initial question...

Is it beneficial to use these codon bias tables to design oligos for
cloning related proteins, or am i just reducing the likelihood of getting a
hit?  



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