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BMC Bioinformatics. 2015 Mar 12;16:79. doi: 10.1186/s12859-015-0517-0.

micropan: an R-package for microbial pan-genomics.

Author information

1
Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway. lars.snipen@nmbu.no.
2
Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway. kristian.liland@nofima.no.
3
Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430, Ås, Norway. kristian.liland@nofima.no.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

PMID:
25888166
PMCID:
PMC4375852
DOI:
10.1186/s12859-015-0517-0
[Indexed for MEDLINE]
Free PMC Article

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