Smooth

Record added by Jurg Ott (the original Rockefeller list)

2008

The construction of accurate linkage maps is not so much depending on the quality of the mapping software, but mostly on the marker data quality. Missing values and scoring errors can severely influence the calculated marker order. The software tool SMOOTH recognises and removes the most unrealistic data points. This software was used to construct the 10,000 marker potato map. The removal of improbable data point is a good medicine for linkage maps, that is not easily overdosed. One error is more harmfull than ten missing values. The software was never intended as user-friendly software. In these days it would be more useful to re-do the programming of the pascal source code into a perl script. Anyone who takes the initiative to generate such a script is welcomed to contact the authors. SMOOTH works best in close cooperation with mapping algorithm RECORD

• Hans van Os
• Herman van Eck (Laboratory for Plant Breeding, Wageningen University, email: herman.vaneck@wur.nl)

http://www.plantbreeding.wur.nl/UK/software_smooth.html

Pascal

MS-DOS

smooth7.exe

• Van Os, Stam, Visser, Van Eck (2005), “SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data”, Theoretical and Applied Genetics, 112(1):187-194
• Van Os, Stam, Visser, Van Eck (2005), “RECORD: A novel method for ordering loci on a genetic linkage map”, Theoretical and Applied Genetics, 112(1):30-40
• Van Os, Andrzejewski, Bakker, Barrena, Bryan, Caromel, Ghareeb, Isidore, de Jong, van Koert, Lefebvre, Milbourne, Ritter, van der Voort, Rousselle-Bourgeois, van Vliet, Waugh, Visse, Bakke, Van Eck (2006), “Construction of a 10,000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map”, Genetics, 173(2):1075-1087