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(In)dependence of optimal pseudocounts on sample size. (A) Optimal pseudocounts using matrix-based ED. One line indicates one motif, colored by the column-wise average entropy of the original matrix. (B) Optimal pseudocounts using sequence-based ED. (C) Average optimal pseudocount over all motifs. The comparison methods are noted on the right: Mat ED = Matrix-based ED; Mat COS = Matrix-based COS; Seq ED = Sequence-based ED; Seq COS = Sequence-based COS.
