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The McPromoter system output ranges from 0 to 1, and Table 5gives the results for a number of thresholds between 0.98 and 0.8; additional predictions below 0.7 are no longer distinguishable from randomly spaced predictions (see [ 34] for discussion).
Using the core promoter set to retrain the McPromoter TSS prediction tool
When we used the version of McPromoter that includes analysis of the physical properties of the genomic DNA, as we do with Drosophila , the true positives are much less correlated with CpG islands (61%), and therefore constitute a broader subset of vertebrate promoters.
When McPromoter was trained on the same, smaller, dataset as NNPP, the reduction in false positives was only about three- to sixfold (data not shown; for details see [ 34]).
By comparison with another predictor for Drosophila promoters, NNPP [ 11], the retrained McPromoter system has 10-15 times fewer false positives, but some of this improvement simply results from the larger training set and not from differences in the underlying algorithm.