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Codon Usage Database specifications


Unique identifier OMICS_08757
Name Codon Usage Database
Restrictions to use None
Maintained Yes


  • person_outline Yasukazu kamura

Publications for Codon Usage Database

Codon Usage Database citations


NS1 codon usage adaptation to humans in pandemic Zika virus

PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] reire/CUB) based on 3803 genes identified as housekeeping (), which are strongly and uniformly expressed in 16 humans tissues. Moreover, we calculated CAI for Ae. aegypti using the table available in Codon Usage Database ( Importantly, the CAI values obtained with our table based on housekeeping genes were very similar to those found with the table from Codon Usage […]


Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

PMCID: 5915587
PMID: 29691381
DOI: 10.1038/s41426-018-0079-0

[…] host species (Homo sapiens, Canis familiaris, Felis catus, and Gallus gallus). The host data were extracted from the Codon Usage Database ( The CAI value by reference codon usage database of the different potential hosts ranged from 0 to 1. The calculation method was performed as previously described (, and the five non-bias codo […]


In silico design and expression of a novel fusion protein of HBHA and high antigenic region of FAP P of Mycobacterium avium subsp. paratuberculosis in Pichia pastoris

PMCID: 5762988
PMID: 29417085
DOI: 10.22099/mbrc.2017.26522.1286

[…] for increasing the expression level of the desired protein in Pichia pastoris, using codon optimization tool ( The Pichia pastoris codon usage table was adapted from a codon usage database ( Full-length codon optimized HBHA-FAP gene in pPICK9K yeast transfer vector was synthesized by Biomatik company […]


Somatic mutation driven codon transition bias in human cancer

Sci Rep
PMCID: 5660177
PMID: 29079855
DOI: 10.1038/s41598-017-14543-1

[…] ed by global codon frequency of a specific codon divided by arithmetic mean of global codon frequency of synonym codons. The global codon frequency in a human reference genome was downloaded from the Codon Usage Database ( Using the RSCU values, a difference in RSCU between the major and the minor codon (∆RSCU) is defined as:8ΔRSCU=R1−R2,where R n is the RSCU of a c […]


Boosting isoprene production via heterologous expression of the Kudzu isoprene synthase gene (kIspS) into Bacillus spp. cell factory

PMCID: 5548705
PMID: 28791618
DOI: 10.1186/s13568-017-0461-7

[…] Codon usage analysis was performed, in which the codon usage preference table for each Bacillus spp. (B. subtilis DSM and B. licheniformis) was determined using codon usage database ( Then the P. montana (kudzu) isoprene synthase (kIspS) original sequence of GenBank Accession No. AY316691 was optimized using the online tool opt […]


HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host Genetic Influence

Front Microbiol
PMCID: 5471322
PMID: 28663742
DOI: 10.3389/fmicb.2017.01083

[…] and LTNP env gene sequences were calculated using CodonW (Ver. 1.4.2) software ( (Peden, ). Codon usage frequencies of human host (Homo sapiens) were obtained from the Codon Usage Database ( (Nakamura et al., ). […]


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Codon Usage Database institution(s)
Laboratory of Gene Structure 2, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

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