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Software . 2024
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Software . 2024
License: CC BY
Data sources: Datacite
ZENODO
Software . 2024
License: CC BY
Data sources: Datacite
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CodonInfo: an R package to analyze codon frequencies

Authors: Martinez, Octavio;

CodonInfo: an R package to analyze codon frequencies

Abstract

Interested in the use of codons in one or more species? Then you could use the CodonInfo R package to study properties of these data. In particular, the package presents and exemplify a coefficient to estimate Codon Bias that varies between zero -when all codons for a given amino acid are used at the same frequency, up to one, when a single codon is employed for a particular species. The package contains a sample of raw codon frequencies for 35 species, as well as a set of functions to estimate in detail the properties of those data in the context of the genetic code. Even when the (nuclear) genetic code is universal, each taxon, at species or higher level, presents particularities in the frequency of codon use (codon bias), or even in the use of different bases within codons. Using Shannon’s entropy formula under different hypotheses it is possible to estimate and dissect the information present in different strata within each species. The first step to explore and use the CodonInfo package is to install it within your R environment; please see file "_Readme_CodonInfo.txt". Then you could read and follow the guide of the package, which is in the document "CodonInfoGuide.pdf". That guide presents the basic concepts needed to estimate and understand the different uses of the data and functions in the package, preparing the reader to make relevant comparisons between species. I am preparing a document to demonstrate the inclusion of data from any species into the package. That document ("IncludeFurtherDataInCodonInfo.pdf") will be available here as soon as possible. I am also preparing a manuscript entitled "Sampling informational properties of codon use through the tree of life" which will be available also here as soon as it is published. Finally, I will very much welcome the possibility to collaborate with researchers interested in this topic; if that is your case, please send me an e-mail to octavio.martinez@cinvestav.mx with subject "Collaboration in codon use".

Keywords

genetic code, codon use, codon bias, codon

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
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Average