Enter your DNA or RNA sequence into the Codon Usage Calculator, select a Genetic Code Table and Reference Organism, and get a full breakdown of your Total Codons Analyzed alongside GC Content, Rare Codons, and Unique Codons Used — so you know exactly how your sequence stacks up against your target organism's preferences.
Total Codons Analyzed
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GC Content
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Rare Codons
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Unique Codons Used
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Codon usage analysis examines the frequency of different codons in coding sequences. It's crucial for protein expression optimization, as organisms have preferences for certain synonymous codons, affecting translation efficiency and protein yield.
RSCU measures the relative usage of synonymous codons. An RSCU value of 1.0 indicates equal usage among synonymous codons, while values >1.0 suggest preference and <1.0 indicate underuse of that codon.
Rare codons are those used infrequently by the organism. High rare codon content can reduce protein expression efficiency and may cause ribosome stalling during translation.
Use the Standard genetic code for most organisms. Select mitochondrial codes for organellar sequences or specific organism tables based on your expression system or study organism.
Yes, you can input multiple sequences in FASTA format. The calculator will analyze all sequences together and provide combined codon usage statistics.
GC content affects codon choice and can influence mRNA stability, translation efficiency, and protein expression levels. Different organisms have varying GC preferences.
By identifying rare codons and codon bias, you can optimize sequences for specific expression hosts, potentially improving protein yield by replacing rare codons with preferred alternatives.