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Table 2 Running time comparison on the challenging instances of the planted motif problem (DNA, |Σ| = 4, N = 20 sequences of length n = 600). Problem instances are denoted by (k,m, |Σ|), where k is the length of the motif implanted with m mismatches.

From: Efficient motif finding algorithms for large-alphabet inputs

Motif problem instances (k, m, |Σ|)

Algorithm

(9,2,4)

(11,3,4)

(13,4,4)

(15,5,4)

(17,6,4)

(19,7,4)

Stemming

0.95

8.8

31

187

1462

8397

MITRA [5]

0.89

17.9

203

1835

4012

n/a

PMSPrune [10]

0.99

10.4

103

858

7743

81010

RISOTTO [6]

1.64

24.6

291

2974

29792

n/a