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Table 7 Parameters values for the simulation of three motif operations.

From: Evaluating deterministic motif significance measures in protein databases

Operation T P F P Length Num gaps
Generalization [25, 50] 5 5 [1, 4]
Specialization [5, 25] 5 5 [1, 4]
Extension 40 5 [5, 10] [1, 9]
  1. Three motif operations – generalization, specialization and length extension – are simulated through the generation of motif information with different parameter values. Generalization and specialization are controlled through the true positive rate, with a fixed false positive and fixed number of concrete symbols (length). Extension is controlled by the length parameter. The number of gaps is calculated for the respective range and proportionally to the length of the motif.