restriction sites and gene synthesis

David Womble dwomble at cmb.biosci.wayne.edu
Fri Jan 26 10:01:42 EST 1996

Martin Stone (mastone at indiana.edu) wrote:
: I am trying to design the sequences of oligonucleotides to use for
: synthesis and expression of a gene. Can somebody please help me with the
: following two issues.

: (1) Does anybody have any suggestions about a codon usage table available
: in gcg that has worked well for gene expression in E. coli? I want to
: optimize the sequence of my DNA to get maximum expression levels.

The codon usage table ecohigh.cod is derived from "highly expressed
enteric bacterial genes".  I don't think it's optimized for expression,
just empirical tabulation of known highly expressed genes.  Do a
fetch ecohigh.cod
to retrieve a copy of the table to examine.

: (2) Is there any way in gcg of getting a list of restriction sites that
: could potentially be introduced into a DNA sequence without changing the
: amino acid sequence of the protein encoded by the DNA.

You can use the map program with the -silent switch, as in: map -sil

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