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
