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BMC Genetics

, 17:62

Statistical and computational genetics


BackgroundDetermination of microsatellite lengths or other DNA fragment types is an important initial component of many genetic studies such as mutation detection, linkage and quantitative trait loci QTL mapping, genetic diversity, pedigree analysis, and detection of heterozygosity. A handful of commercial and freely available software programs exist for fragment analysis; however, most of them are platform dependent and lack high-throughput applicability.

ResultsWe present the R package Fragman to serve as a freely available and platform independent resource for automatic scoring of DNA fragment lengths diversity panels and biparental populations. The program analyzes DNA fragment lengths generated in Applied Biosystems® ABI either manually or automatically by providing panels or bins. The package contains additional tools for converting the allele calls to GenAlEx, JoinMap® and OneMap software formats mainly used for genetic diversity and generating linkage maps in plant and animal populations. Easy plotting functions and multiplexing friendly capabilities are some of the strengths of this R package. Fragment analysis using a unique set of cranberry Vaccinium macrocarpon genotypes based on microsatellite markers is used to highlight the capabilities of Fragman.

ConclusionFragman is a valuable new tool for genetic analysis. The package produces equivalent results to other popular software for fragment analysis while possessing unique advantages and the possibility of automation for high-throughput experiments by exploiting the power of R.

KeywordsFragment analysis Genetic markers R package Least squares Open source software AbbreviationsBpbase pair

DNADeoxyribonucleic acid

FAM, HEX, NED, ROX and PETdyes used for DNA sequencing. All four dyes can be excited at a single wavelength 488 nm, but emit at distinctly different wavelengths

FSAFile associated with Applied Biosystems, usually output of DNA fragment analysis. A type of FASTA file format

MAFminor allele frequency

M13universal primer for multiplexing

SNPsingle nucleotide polymorphisms

SSRsimple sequence repeat

Electronic supplementary materialThe online version of this article doi:10.1186-s12863-016-0365-6 contains supplementary material, which is available to authorized users.

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Autor: Giovanny Covarrubias-Pazaran - Luis Diaz-Garcia - Brandon Schlautman - Walter Salazar - Juan Zalapa


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