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Table 2 Motif discovery methods summary.

From: Discovering multiple realistic TFBS motifs based on a generalized model

Representations
(i) Consensus
(ii) Matrix and Evaluations
(a) Enumerations (b) Stochastic Search
   Exhaustive Non-exhaustive Local Global
      Single-point (Gibbs Sampling) Multi-point (GAs)
(i) Hamming [7, 8] [14] [17, 18]   [9, 10]
  Z-score   Weeder [15, 16]    [24]
(ii) IC   [41]   [46] [10], GALF-P [28]
  Bayesian   BioOptimizer [40]   BioProspector [19]
Motif Sampler [21]
GAME [27]
  MAP    MEME [12]
MDScan [5]
AlignACE [20]  
  1. Summary of the representative motif discovery methods. The methods included in our comparison experiments are shown with their names. IC stands for Information Content.