CodonTuner

CodonTuner is an interactive codon optimization tool. Rather than returning a single fixed result, it allows individual codons to be edited directly, or target ranges to be specified across multiple metrics — CAI, GC content, ENC, and tAI — with results updated in real time.

Supported organism: Escherichia coli (K-12)

Where the data comes from

CAI / GC / ENC are calculated using genome-wide E. coli K-12 codon usage frequencies.

tAI uses real E. coli K-12 tRNA gene copy numbers from dos Reis et al. (2004), cross-verified against GtRNAdb, with standard wobble rules including inosine wobble for tRNA-Arg, the sole case of inosine modification documented in bacteria. E. coli's cmo5U modification is not modeled.

ENC uses the full Wright (1990) degeneracy-class-weighted formula (grouping amino acids by 2/3/4/6- fold codon family size), with the standard correction for sequences missing Ile data.

Feedback

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