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Publisert 2015

Les på engelsk


Tidsskrift : BMC Bioinformatics , vol. 16 , p. 1–8 , 2015

Utgiver : BioMed Central (BMC)

Internasjonale standardnummer :
Trykt : 1471-2105
Elektronisk : 1471-2105

Publikasjonstype : Vitenskapelig artikkel

Bidragsytere : Snipen, Lars-Gustav; Liland, Kristian Hovde

Sak : 1

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Kjetil Aune


A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single genome. Studies of pan-genomes have become popular due to the easy access to whole-genome sequence data for prokaryotes. A pan-genome study reveals species diversity and gene families that may be of special interest, e.g because of their role in bacterial survival or their ability to discriminate strains.

We present an R package for the study of prokaryotic pan-genomes. The R computing environment harbors endless possibilities with respect to statistical analyses and graphics. External free software is used for the heavy computations involved, and the R package provides functions for building a computational pipeline.

We demonstrate parts of the package on a data set for the gram positive bacterium Enterococcus faecalis. The package is free to download and install from The Comprehensive R Archive Network.