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CodonO specifications


Unique identifier OMICS_08755
Name CodonO
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Xiu-Feng Wan <>

Publication for CodonO

CodonO in publications

PMCID: 5735904
PMID: 29270250
DOI: 10.1186/s40793-017-0290-y

[…] and 10.1601/nm.1804 cm13 (nz_cp017420), a close representative of the host 10.1601/nm.1804 10.1601/strainfinder?urlappend=%3fid%3darb+1. the average codon usage bias calculation was performed using codono web server ( []. 10.1601/nm.1804 cm13 (nz_cp017420) and phage rg-2014 had similar average codon usage bias of 0.440141 and 0.406048, respectively, […]

PMCID: 4490425
PMID: 26016504
DOI: 10.3390/ijms160611996

[…] ( scuo (synonymous codon usage order) was developed based on “shannon information theory” [] and varied from 0 (no bias) to 1 (most bias). it is calculated using “codono” software [] as 1 minus the ratio of expected to observed entropy, where the expected value of entropy assumes random usage of all synonymous codons of a given amino acid., two null models […]

PMCID: 4408588
PMID: 25887254
DOI: 10.1186/s12864-015-1393-8

[…] and the remaining 50% of medium-length genes. translation efficiency is also known to be affected by codon usage, so we included synonymous codon usage order (scuo), which was obtained from the codono platform []; higher values indicate more codon bias, meaning less random codon use in a gene’s coding region. the three gene groups significantly differ in transcript level, translational […]

PMCID: 4176184
PMID: 25200075
DOI: 10.1093/nar/gku811

[…] in a given sequence (ew) scaled from 0 to 1. we considered the bias to equal (1 - ew), thus high entropy in codon usage equated to low bias and vice versa. this method is nearly identical to the codono metric (synonymous codon usage order) proposed by wan et al. () and differ only in their methods of computing relative entropy according to roth et al. (). the codon bias calculation of suzuki […]

PMCID: 3825069
PMID: 24255825
DOI: 10.1186/2193-1801-2-492

[…] using mega version 5.1 (). enc values and cai were calculated for all pcg by using online codonw ( and cai calculator 2 (). scuo was computed using standalone codono ()., coa is a multivariate statistical method used to identify major factors, shaping scu patterns across genes and plot genes according to various influencing factors of scu (). multivariate […]

CodonO institution(s)
Systems Biology Laboratory, Department of Microbiology, Miami University, Oxford, OH, USA

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