Table 3.
Comparison of approaches
| Enum. | Prob. | Nat. | Com. | |
|---|---|---|---|---|
| Solution technique | Exhaustive | Heuristic | Meta-heuristic | ? |
| Can deal with a big data set | × | ✓ | ✓ | ? |
| Is it fast? | × | ✓ | ? | ? |
| Can it find long motif? | × | ✓ | ✓ | ✓ |
| Is it a global search? | ✓ | × | ✓ | ? |
| Low number of required parameters | × | ✓ | ? | ? |
| Representation | Consensus | PWM | Flexible | Flexible |
| Can it find all motifs? | ✓ | × | ? | ? |
| Can it find weak motifs? | × | ✓ | ? | ? |
| Degenerate positions | Limited | Flexible | Flexible | ? |
| Objective function | Flexible | Flexible | Flexible | Flexible |
| Is it a simple concept? | ✓ | × | ✓ | ? |
| Derivation-free mechanism | × | × | ✓ | ? |
Hint: Question mark means maybe yes or no, Enum., prob., Nat., and Com. are standing for Enumerative, Probabilistic, Nature-inspired and Combinatorial, respectively.