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Kheradpour et al. mained unclear what fraction of conserved motif instances were functional and what fraction of functional instances were conserved, namely, whether in fact comparative genomics is applicable for high-specificity and high-sensitivity identification of individual motif instances. Moreover, the available genomes have been either too few for sufficient neutral divergence or too distantly related for motif instances to be conserved (e.g., Cooper et al. 2005; Ettwiller et al. 2005). Accurate motif instance identification would thus require many closely related species, which also present novel conceptual and methodological challenges, with respect to sequence coverage, alignment accuracy, an

Year: 2011
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