rare codon calculator | CLARK LAB @ NOTRE DAME


The Rare Codon Calculator

Results from the Rare Codon Calculator should cite:
Clarke T.F. & Clark P.L. (2008) Rare Codons Cluster PLoS ONE 3: e3412
This article is freely accessible at the PLoS ONE Website.

Interpreting Your Results

What the %MinMax algorithm does: %MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the %MinMax algorithm works.

%MinMax results are averaged over an 18-codon sliding window; hence the result for "codon window = 1" is the average codon usage for codons 1-18, codon window 2 = codons 2-19, etc.

What the %MinMax algorithm does not do: The %MM algorithm provides information on the frequency and distribution of rare and common codons. %MinMax does not explicitly predict local translation rate. Experimentally, it has been observed that rare codons can lead to a reduced local translation rate (again, see the PLoS ONE paper), but the correlation is not perfect.

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