A summary of experiments with synthetic data tests for high quality TRANSFAC™ matrices.

The results for Match™ and optimized matrices (OPT) are organized in blocks. Match™ consists of three tested types of settings: “min FP” - minimum number of false positives; “min FN” - minimum number of false negatives; “both crit.” - min of sum of both criteria; “m” and “di” - refer to the number of hits after the application of mono- and dinucleotide matrices, respectively. TP rows show the number of retrieved TP hits (out of number showed in test size). Cut-off values for optimized matrices were selected as they appeared after optimization.