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Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables using the E. coli preferences, for example.

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This sounds like jcat.de –  bobthejoe Apr 23 '12 at 22:24
    
That tool is pretty much what I was going for. Thank you. –  leonardo Apr 24 '12 at 0:04
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helixweb.nih.gov/dnaworks also has this functionality. It also accepts information from the Codon Usage Database. However, I'll love to see any improvements in the field. –  bobthejoe Apr 24 '12 at 2:42
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up vote 5 down vote accepted

Try the Codon Usage Database at Kazusa. You can search by organism. The database contains 35,799 organisms and compiled from 3,027,973 complete protein coding genes (CDS's), but last updated in 2007.

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This kind of database is what I was looking for in terms of access. JCat seems like a good tool to do the work for me, but I'd like to try it myself using this database. –  leonardo Apr 24 '12 at 0:05
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Plenty of softwares doing that kind of functionality. A 2007 open access review lists >30 such softwares http://www.ncbi.nlm.nih.gov/pubmed/17882154. However, No correlation between 'most common' codon and recombinant protein expression yield. http://www.ncbi.nlm.nih.gov/pubmed/21102527. Thus, those >30 softwares are pointless.

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The second conclusion is interesting. I would have thought perhaps it would make a difference when using microbes as bioreactors and the only quantifiable trait that matters is the yield. –  leonardo Apr 24 '12 at 20:10
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