Table 3 Nineteen motif finders used in the assessment. An x mark associates a sequence dataset with a tool. The sequence datasets are grouped by species. Thirteen tools in italic face are older tools used by Tompa et al. [29]. The rest are newer tools. The datasets with (*) were used to run newer tools

Tool Name

hm01g*

hm04g*

hm08m

hm15g*

hm17g*

hm19g*

hm22g*

hm22m

mus04m

mus06g

mus10g

mus11m

yst02g

yst03m

yst06g

yst09g*

Ref.

AlignACE

x

x

x

x

x

x

29

ANN-Spec

x

x

x

x

x

x

x

x

x

29

ChIPMunk

x

x

x

x

x

x

x

31

Consensus

x

x

x

x

x

29

DMINDA

x

x

x

x

x

x

x

32

GLAM

x

x

x

x

x

x

x

x

x

29

Improbizer

x

x

x

x

x

x

x

x

x

29

MEME (older version)

x

x

x

x

x

x

x

x

29

MEME (v. 4.11.4)

x

x

x

x

3

MITRA

x

x

x

x

x

x

x

x

x

29

MotifSampler

x

x

x

x

x

x

x

x

29

oligodyad-analysis

x

x

x

x

x

x

x

x

29

peak-motifs

x

x

x

x

x

x

x

33

QuickScore

x

x

x

x

x

x

29

SeSiMCMC

x

x

x

x

x

x

x

x

x

29

STEME

x

x

x

x

34

Weeder

x

x

x

x

x

x

x

x

x

29

XXmotif

x

x

x

x

35

YMF

x

x

x

x

x

x

x

x

x

29