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SNP Detection in A. thaliana

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

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Gabriele Schweikert, Ph.D.

As part of the resequencing project for 20 diverse strains of the model plant Arabidopsis thaliana, I have developed a SVM-based method for accurate detection of single-nucleotide polymorphisms (SNPs) from hybridization data. We have thus identified more than 1 million SNPs. Assessing the effects of the nonredundant SNPs on the annotated protein-coding genes we have found many that have a large impact on gene integrity, e.g. more than 1000 SNPs introduce premature stop codons.

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Publications

Clark, R, Schweikert, G, Toomajian, C, Ossowski, S, Zeller, G, Shinn, P, Warthmann, N, Hu, T, Fu, G, Hinds, D, Chen, H, Frazer, K, Huson, D, Schölkopf, B, Nordborg, M, Rätsch, G, Ecker, J, and Weigel, D (2007).
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana
Science, 317(5836):338 - 342.
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