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CodonInfo: an R package to analyze codon frequencies

Artículo

 

Te invitamos a leer el artículo "CodonInfo: an R package to analyze codon frequencies" publicado en Zenodo, ​a cargo del profesor investigador de la Unidad de Genómica Avanzada del Cinvestav Dr. Octavio Martínez de la Vega, Profesor Investigador de la UGA.

Autores: Octavio Martínez 

  1. Laboratorio de Biología Computacional de la Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados (Cinvestav), Irapuato 36824, Guanajuato, Mexico

Felicidades por su arduo trabajo.

Summary:

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".


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13/06/2023 01:20:42 p. m.