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CodonO specifications

Information


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

Maintainer


  • person_outline Xiu-Feng Wan

Publication for CodonO

CodonO citations

 (8)
library_books

Complete genome sequence of lytic bacteriophage RG 2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB 1

2017
Stand Genomic Sci
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 (http://sysbio.cvm.msstate.edu/codono/) []. 10.1601/nm.1804 cm13 (nz_cp017420) and phage rg-2014 had similar average codon usage bias of 0.440141 and 0.406048, respectively, […]

library_books

A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA Seq Data

2015
Int J Mol Sci
PMCID: 4490425
PMID: 26016504
DOI: 10.3390/ijms160611996

[…] (http://codonw.sourceforge.net). 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 […]

library_books

Pichia pastoris regulates its gene specific response to different carbon sources at the transcriptional, rather than the translational, level

2015
BMC Genomics
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 […]

library_books

Synonymous codon bias and functional constraint on GC3 related DNA backbone dynamics in the prokaryotic nucleoid

2014
Nucleic Acids Res
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 […]

library_books

Mutational pressure dictates synonymous codon usage in freshwater unicellular α cyanobacterial descendant Paulinella chromatophora and β cyanobacterium Synechococcus elongatus PCC6301

2013
Springerplus
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 (http://codonw.sourceforge.net) 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 […]

library_books

Comparative Analysis of Codon Usage Bias and Codon Context Patterns between Dipteran and Hymenopteran Sequenced Genomes

2012
PLoS One
PMCID: 3422295
PMID: 22912801
DOI: 10.1371/journal.pone.0043111

[…] random usage of all synonymous codons of a given amino acid. codon usage bias calculated by this approach is suitable for comparative analysis of codon usage bias within and between genomes . the ‘codono’ software was used to calculate the scuo index of each gene in each of the 22 species. as scuo values vary from 0 (no bias) to 1(most bias), we categorized low and high biased genes based […]


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

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