IUBio

bovine codon

Simon Greenberg simong at cc.huji.ac.il
Sat Jun 14 10:11:13 EST 1997


Hi, hope this is what you are really need:
Codon Usage Database compiled from CUTG 
Source: GenBank Release 100 [15 Apr 1997] with 
alphabetical lists of "all" organisms (5579 organisms) 
More info you can get from:

http://www.dna.affrc.go.jp/~nakamura/index.html

Good luck.
                     Sincerely yours,  Simon Greenberg

Hebrew   University  of  Jerusalem| Internet: simong at gene.md.huji.ac.il
Medical School, Computation Center| WWW     : http://gene.md.huji.ac.il/
P.O.Box 12208,    Kiryat  Hadassah| 
Jerusalem,        Israel  91120   | FAX: 972-2 6784-010 & 972-2 6436-892

Todd Ellermann wrote:
> 
> Thank you in advance for your response.
> 
>         I am a student worker at the University of Arizona working in the
> Biotech Computing Facility. Somehow this problem has ended up in my lap
> and I don't have a clue how to solve it.
>         I have a user who has sent me the following request:
> 
> What I was asking for is this: since you work for the Biotech
> COmputing Facility, you must be familiar with the GCG programs. When one
> uses the BACKTRANSLATION program to backtranslate a peptide sequence
> (known) to its potential cDNA sequence (unknown), the program in its
> third step asking for:
> 
>         Use what codon frequency file (* GenRunData: ecohigh.cod *) ?
> 
> I believe the default is a codn file for E. coli. I need the equivalent
> file for Bovine.
> 
> Does anyone know where I might find a bovine.cod file for this user to
> use. I have done some web searches and have looked through the gcg disks
> and found nothing. Does the user somehow need to enter the data himself?
> Or is there a site out there that would have such a data file? How do I
> install it once I get it?
>         I am somewhat familiar with GCG (I do the database updates etc..
> , but as far as the user side goes I have little to no knowledge. )
> 
> Thank you again.
> Todd Ellermann
> todde at aretha.biosci.arizona.edu



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