I'm trying to optimize the codon in my sequence for E coli BL21 and Rosetta 2 cells, which codon usage table should i use for this strain? Thank you!
Dear Jonathan Jonathan
you have to use the E. coli codon usage
Also if BL21 are E.coli B and not K-12 there are not main differences between the 2 codon usages.
if you would like to do it by yourself you can use
http://www.jcat.de/
however the most of company that provide synthetic DNA (ag Genescript) provides also with out any charge a codon optimization service.
Some people think that codon optimization, that remove all the rare codons may speed up to much the protein expression rate and it is better to maintain some rare codon, since this are present also in the E.coli proteins.
Theoretically Rosetta are designed to supply to codon bias. If you are working with a codon optimized gene. you can use directly the BL21 cells.
best regards
Manuele
Dear Manuele Martinelli ,
thank you for the reply, I accidentally misrepresented my question (It's should not be BL21 "and" Rosetta 2, I mentioning Rosetta 2 for the comparison since Rosetta 2 with CamR in pRARE slow down the growth rate bcs of the Cam exsistence in the media.)
once again, thank you Manuele for the suggestion, I will contact the company that I work with for the codon optimization.
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