A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression array: Transcript and Genome Hybridizations

The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

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Horiuchi Y, Harushima Y, Fujisawa H, Mochizuki T, Kawakita M, Sakaguchi T, Kurata N