Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction by Xuhua Xia

“…Here I review PWM-based methods used in motif characterization and prediction (including a detailed illustration of the Gibbs sampler for de novo motif discovery), present statistical and probabilistic rationales behind statistical significance tests relevant to PWM, and illustrate their application with real data. The multiple comparison problem associated with the test of site-specific frequencies is best handled by false discovery rate methods. …”
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