Are the objective functions informative?
The first step to design a new algorithm for the motif discovery problem is to choose a proper objective function. This is critical because the objective function implements the designer’s understanding of the protein-DNA interaction model. Searching for candidates that optimize the objective function is a major step to pull out the candidate binding sites from the background sequences. An ideal objective function should be able to assign the optimal score to the true motif binding sites and nowhere else. Although there are numerous tools available, surprisingly the types of objective functions are not as many. Here we examined three popular objective functions. Theoretically, for each objective function we would test whether the score of the planted binding sites is superior to the scores of all other sets of words in the background sequences which are false positive predictions. This, of course, is impractical. In practice, we chose one tool that applies this objective function and c
