Codon preferences

Derek Parsonage dp at invader.bgsm.wfu.edu
Wed Nov 27 11:04:40 EST 1996


In article <9610258489.AA848949980 at uu1500.epitope.com>,
jkellogg at epitope.com ("Jill Kellogg") wrote:

> Dear Netters,
> 
> I would like to make a file, based on peptide sequences in the Swis-Prot
> database, that would show the codon preferences of a single species, e.g. homo
> sapiens.  That is the program would be able to look at all the Homo sapien
> protein sequences and tabulate the usage of each codon.  However, I
can't find a
> program capable of determining codon preferences and displaying those
> preferences.  If anyone knows of a program like this please let me know.
> 
> Thanks, Jill
> jkellogg at epitope.com

There is a web page giving codon usage tables at
http://www.dna.affrc.go.jp/~nakamura/CUTG.html

The tables are generated from GenBank, but if you only want Swiss-Prot
maybe you can do some editing, or talk to the people running the site.
Hope this helps

-- 
Derek Parsonage                        Wake Forest University
Dept. of Biochemistry                     Medical Center
dp at invader.bgsm.wfu.edu                 Winston-Salem NC  USA                                                               



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