On Fri, 2011-09-30 at 10:17 -0500, Craig A. Bingman wrote: > This is quite different than being explicitly optimized to express > mammalian proteins.
Sure - what I meant was optimized codon usage. I guess to answer the original question, one could use rare codon calculator http://nihserver.mbi.ucla.edu/RACC/ and then see if the addition of tRNAs for AGA, AGG, AUA, CUA, GGA, CCC, and CGG in Rosetta2 would solve the problem for a particular sequence. (It's likely that Pat has done that already). I don't know if those cover all the rare codons in E.coli or if there is something in yeast sequence that is still missing and thus adjusting the codon usage will help. In theory, if the rare codons are all covered by Rosetta's extra tRNAs, codon optimization should not make any difference. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
