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looking for unfavouable codon usage

Barbara Dunn bdunn at GENOME.STANFORD.EDU
Mon Oct 23 16:22:30 EST 1995

On 22 Oct 1995, H.p.r. Law [bic] wrote:

> Can any one tell me what is the best way to check for 
> favourable/unfavourable codon usage? I have trouble expressing an 
> open reading frame (about 1.7 Kb) in the E.coli T7 expression 
> system. Thanks in advance!
> Ruby Law

You can get the codon usage tables for many organisms by accessing the
gopher server:  genome-gopher.stanford.edu

then select --> 7.  FTP Archives for Molecular Biology/

then select --> 5.  Codon Usage Tables (Massachusetts General Hospital)/

and then select whichever organism you want... 

the E. coli file is --> 15.  eco.cod 

the S. cerevisiae file is --> 48.  ysc.cod

In addition, you can access the following Web URL's for even more recent 
codon usage statistics from the CUTG database (from Yasukazu Nakamura): 

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

Hope this has helped, 

 Barbara Dunn, Ph.D., Database Curator

 Saccharomyces Genome Database
 Department of Genetics                Internet contacts for SGD:
 Stanford University Med. Ctr.         WWW:     http://genome-www.stanford.edu/
 Stanford, CA  94305-5120   USA        Gopher:  genome-gopher.stanford.edu
 phone: 415-725-8956                   ftp:     genome-ftp.stanford.edu
 fax:   415-723-7016
 e-mail:  bdunn at genome.stanford.edu

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