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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]