Efficient and accurate construction of genetic linkage maps from noisy and missing genotyping data

Authors:
Yonghui Wu;Prasanna Bhat;Timothy J. Close;Stefano Lonardi
Affiliations:
Dept. of Computer Science and Eng., University of California, Riverside, CA;Dept. of Botany & Plant Sciences, University of California, Riverside, CA;Dept. of Botany & Plant Sciences, University of California, Riverside, CA;Dept. of Computer Science and Eng., University of California, Riverside, CA
Venue:
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Year:
2007

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Abstract

We introduce a novel algorithm to cluster and order markers on a genetic linkage map, which is based on several theoretical observations. In most cases, the true order of the markers in a linkage group can be efficiently computed from the minimum spanning tree of a graph. Our empirical studies confirm our theoretical observations, and show that our algorithm consistently outperforms the best available tool in the literature, in particular when the genotyping data is noisy or in case of missing observations.