The BBLS methods had much better ROC-50 scores though; BBLS MS was better than PWM, MS, and WS (p-values 0.007, 0.092, and 0.007) and BBLS PWM was also better than these three methods, though the differences were borderline significant (all p-values 0.065).
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A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.
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