Rep : restriction sites and gene synthesis

FERRAN,edgardo Edgardo.FERRAN at TLS1.elfsanofi.fr
Fri Jan 26 06:16:19 EST 1996


> (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 frequency table that GCG uses by default is just the table for ecoli:
ecohigh.cod (enteric bacterial highly-expressed genes, 7/19/83). This is the table
placed in the genrundata directory (gcg/gcgcore/data/rundata). 
Other tables are placed in the genmoredata directory (celegans_high.cod,
celegans_low.cod, human_high.cod, etc.).

> (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.

Try the map command with the -silent parameter.

Edgardo Ferran
Sanofi Recheche
Labege, France

e-mail: edgardo.ferran at tls1.elfsanofi.fr




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