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Findings from B. Pfeifer and Co-Authors Reveals New Information on Molecular Biology (PopGenome: An Efficient Swiss Army Knife for Population Genomic...

August 26, 2014



Findings from B. Pfeifer and Co-Authors Reveals New Information on Molecular Biology (PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R)

By a News Reporter-Staff News Editor at Life Science Weekly -- Investigators publish new report on Life Science Research. According to news reporting originating in Dusseldorf, Germany, by NewsRx journalists, research stated, "Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches."

The news reporters obtained a quote from the research, "Here, we present PopGenome, a population genomics package for the R software environment (a de facto standard for statistical analyses). PopGenome can efficiently process genome-scale data as well as large sets of individual loci. It reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in most common formats, including those used by the HapMap, 1000 human genomes, and 1001 Arabidopsis genomes projects. PopGenome also reads associated annotation files in GFF format, enabling users to easily define regions or classify SNPs based on their annotation; all analyses can also be applied to sliding windows. PopGenome offers a wide range of diverse population genetics analyses, including neutrality tests as well as statistics for population differentiation, linkage disequilibrium, and recombination. PopGenome is linked to Hudson's MS and Ewing's MSMS programs to assess statistical significance based on coalescent simulations. PopGenome's integration in R facilitates effortless and reproducible downstream analyses as well as the production of publication-quality graphics. Developers can easily incorporate new analyses methods into the PopGenome framework."

According to the news reporters, the research concluded: "PopGenome and R are freely available from CRAN (http://cran.r-project.org/) for all major operating systems under the GNU General Public License."

For more information on this research see: PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R. Molecular Biology and Evolution, 2014;31(7):1929-1936. Molecular Biology and Evolution can be contacted at: Oxford Univ Press, Great Clarendon St, Oxford OX2 6DP, England. (Oxford University Press - www.oup.com/; Molecular Biology and Evolution - mbe.oxfordjournals.org)

Our news correspondents report that additional information may be obtained by contacting B. Pfeifer, Cluster Excellence Plant Sci, Dusseldorf, Germany. Additional authors for this research include U. Wittelsburger, S.E. Ramos-Onsins and M.J. Lercher (see also Life Science Research).

Keywords for this news article include: Europe, Germany, Dusseldorf, Life Science Research

Our reports deliver fact-based news of research and discoveries from around the world. Copyright 2014, NewsRx LLC


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Source: Life Science Weekly


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