Table 2 Parameter settings for performance comparison among eight motif finding methods
From: A systematic approach to RNA-associated motif discovery
Motif finding tools | Motif search size range | E-value or p-value threshold | Background model | Reference |
|---|---|---|---|---|
MDS2 | k ≥ 2 | 0.05 | Large-scale sampling |  |
MEME | 2 ≤ k ≤ 50 | 0.05 | 0-order Markov Model | [15] |
DREME | – | 0.05 | K di-nucleotide shuffled input sequences | [43] |
COSMO | 2 ≤ k ≤ 8 | – | 0-order Markov Model | [16] |
Improbizer | 3 ≤ k ≤ 20 | – | 0-order Markov Model | [38] |
MERCI | – | 0.05 | K di-nucleotide shuffled input sequences | [60] |
DMINDA 2.0 | k ≥ 6 | 0.05 | – | [61] |
MotifClick | k ≥ 4 | – | – | [47] |