Figure 6.

Running time of the DEME algorithm. The plot shows the CPU time required by DEME on a typical PC using an typical ChIP-chip (positive) dataset, as a function of the number of non-binding probe sequences as the negative set. The positive set contains 59 probe sequences with an average length of 564 nt that bind GCN4 in rich media (the ChIP-chip datasets compiled by Harbison et al. [5] contain on average 40 probe sequences of length 564 nt). Each negative dataset contains randomly selected non-binding probe sequences. The largest negative set studied contains all non-binding probe sequences.