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.
Determining the significance of codon clusters in your results: Turn the "Perform Random Reverse Translation" option to ON. This option will calculate the rare codon distribution in 200 hypothetical gene sequences synonymous to your submitted sequence, constructed using the codon usage database you selected. The average of these 200 RRTs is displayed along with the actual results for your gene sequence. The difference between the actual result and the average RRT determines the significance of the observed codon usage distribution in the actual sequence; the larger the difference, the more significant the result.
Results using CHARMING should cite:
Rodriguez A., Wright G., Emrich S.J. & Clark P.L. (2018) %MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding Protein Sci. 27: 356-362
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