Rare Codon Calculator (RaCC)
Over-expression of recombinant protein in E. coli may be severely diminished (to the point of being undetectable) if the ORF that codes for the protein uses "rare" codons that are infrequently used by E. coli. In particular, codons for arginine (AGG, AGA, CGA), leucine (CTA), isoleucine (ATA), and proline (CCC) may be a problem. For instance, the presence of more than ~ 8-9 of the two rarest Arg codons (AGG and AGA), particularly back-to-back as a tandem repeat, has prevented over-expression of Pyrobaculum aerophilum proteins in our lab. RaCC will determine the number of rare E. coli codons in a DNA sequence.
