Fragman: an R package for fragment analysis.
BACKGROUND
Determination 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.


RESULTS
We 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.


CONCLUSIONS
Fragman 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.
Department of Horticulture, University of Wisconsin, Madison, WI, USA. cova_ruber@live.com.mx.
Giovanny
G
Covarrubias-Pazaran
Department of Horticulture, University of Wisconsin, Madison, WI, USA.|Instituto Nacional de Investigaciones Forestales, Agricolas, y Pecuarias, Campo Experimental Pabellon, Aguascalientes, Mexico.
Luis
L
Diaz-Garcia
Department of Horticulture, University of Wisconsin, Madison, WI, USA.
Brandon
B
Schlautman
Department of Horticulture, University of Wisconsin, Madison, WI, USA.
Walter
W
Salazar
Department of Horticulture, University of Wisconsin, Madison, WI, USA. jezalapa@wisc.edu.|USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, USA. jezalapa@wisc.edu.
Juan
J
Zalapa
D000483:Alleles; D002874:Chromosome Mapping; D060005:Genotyping Techniques; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D040641:Quantitative Trait Loci; D012984:Software; D029799:Vaccinium macrocarpon / Q000235:genetics*
Fragment analysis; Genetic markers; Least squares; Open source software; R package