restriction sites and gene synthesis

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Mon Jan 29 13:56:31 EST 1996

In article <mastone-2501961713230001 at piglet.chem.indiana.edu>, mastone at indiana.edu (Martin Stone) writes:
>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.

Look in gendocdata, at the file ecohigh.cod.  This is the codon usage in 
highly expressed E. coli genes.

>(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.

 $ map/silent                      (OpenVMS)
 % map -silent                     (Unix)

Note, it figures out which frame to be silent in by the first base that
you tell it to map, so if the DNA you're working on is out of frame, use
begin=2 or 3. 


David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 

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