DNA & RNA

Codon Usage Calculator

Compute codon usage for a coding sequence: counts, frequency per thousand, fraction among synonymous codons and RSCU, grouped by amino acid. Free and in-browser.

Codon Usage CalculatorRuns in your browser; nothing is uploaded

In-frame coding sequence(s)

Codons counted78

GC at third position57.7%

AA	Codon	Count	/1000	Fraction	RSCU
F	TTT	0	0.0	0.00	0.00
	TTC	1	12.8	1.00	2.00
L	TTA	1	12.8	0.13	0.75
	TTG	2	25.6	0.25	1.50
	CTT	2	25.6	0.25	1.50
	CTC	0	0.0	0.00	0.00
	CTA	1	12.8	0.13	0.75
	CTG	2	25.6	0.25	1.50
S	TCT	0	0.0	0.00	0.00
	TCC	1	12.8	0.11	0.67
	TCA	1	12.8	0.11	0.67
	TCG	2	25.6	0.22	1.33
	AGT	0	0.0	0.00	0.00
	AGC	5	64.1	0.56	3.33
Y	TAT	0	0.0	0.00	0.00
	TAC	0	0.0	0.00	0.00
Stop	TAA	0	0.0	0.00	0.00
	TAG	0	0.0	0.00	0.00
	TGA	0	0.0	0.00	0.00
C	TGT	0	0.0	0.00	0.00
	TGC	1	12.8	1.00	2.00
W	TGG	3	38.5	1.00	1.00
P	CCT	3	38.5	0.43	1.71
	CCC	2	25.6	0.29	1.14
	CCA	1	12.8	0.14	0.57
	CCG	1	12.8	0.14	0.57
H	CAT	2	25.6	1.00	2.00
	CAC	0	0.0	0.00	0.00
Q	CAA	3	38.5	0.75	1.50
	CAG	1	12.8	0.25	0.50
R	CGT	3	38.5	0.30	1.80
	CGC	5	64.1	0.50	3.00
	CGA	0	0.0	0.00	0.00
	CGG	1	12.8	0.10	0.60
	AGA	0	0.0	0.00	0.00
	AGG	1	12.8	0.10	0.60
I	ATT	1	12.8	1.00	3.00
	ATC	0	0.0	0.00	0.00
	ATA	0	0.0	0.00	0.00
M	ATG	2	25.6	1.00	1.00
T	ACT	1	12.8	0.20	0.80
	ACC	3	38.5	0.60	2.40
	ACA	0	0.0	0.00	0.00
	ACG	1	12.8	0.20	0.80
N	AAT	4	51.3	0.80	1.60
	AAC	1	12.8	0.20	0.40
K	AAA	0	0.0	0.00	0.00
	AAG	0	0.0	0.00	0.00
V	GTT	2	25.6	0.50	2.00
	GTC	1	12.8	0.25	1.00
	GTA	1	12.8	0.25	1.00
	GTG	0	0.0	0.00	0.00
A	GCT	0	0.0	0.00	0.00
	GCC	4	51.3	0.67	2.67
	GCA	2	25.6	0.33	1.33
	GCG	0	0.0	0.00	0.00
D	GAT	2	25.6	0.67	1.33
	GAC	1	12.8	0.33	0.67
E	GAA	3	38.5	0.60	1.20
	GAG	2	25.6	0.40	0.80
G	GGT	0	0.0	0.00	0.00
	GGC	2	25.6	1.00	4.00
	GGA	0	0.0	0.00	0.00
	GGG	0	0.0	0.00	0.00

What is codon usage bias?

Most amino acids are encoded by more than one codon. Organisms do not use these synonymous codons equally, and highly expressed genes tend to favour codons that match abundant tRNAs. Codon usage matters when expressing a gene in a different host, for example a human gene in E. coli.

RSCU explained

Relative synonymous codon usage (RSCU) is the observed count of a codon divided by the count expected if all synonymous codons for that amino acid were used equally. RSCU = 1 means no bias; above 1 the codon is preferred; below 1 it is avoided.

Input requirements

Paste an in-frame coding sequence (starting at the first base of a codon). Multiple sequences in FASTA format are pooled. A trailing partial codon is ignored and reported.

Learn the method properly. Python for Bioinformatics: Programming taught through biological problems, from parsing FASTA to tested, shareable tools. View the course.

FAQ

Frequently asked questions

Not answered here? Send us your question and we will reply by e-mail.

This tool reports the usage of your sequence. Comparing with a host table (for example from the Kazusa or CoCoPUTs databases) shows which codons may limit expression.

No. The calculation runs in your browser with JavaScript. Nothing you paste is sent to a server, which makes the tool safe for unpublished or confidential sequences.

What is codon usage bias?

RSCU explained

Input requirements

Frequently asked questions

Can I compare against a host organism?

Is my sequence uploaded anywhere?