127 128 E. P. Xing et al. superior performance on both semi-realistic test data and cis-regulatory sequences from yeast and Drosophila genomes with regard to sensitivity, specificity, flexibility and extensibility. a Not to be confused with model-based motif scan, the task of searching known motifs based on given position weight matrices, as addressed by Frith et al. 10 and Huang et al. 15 c Heuristics are generally employed -such as throwing away overlapping sampled motifs (in the Gibbs

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... ) or rescaling the joint posterior of x (in MEME) -to enforce the non-overlapping constraint. Nevertheless, this results in inconsistencies between the computed motif distribution and the one defined by the model, and incurs a sizable overhead due to wasteful computations.