Table 4

Motif recognition on biological data.

Data set

Published motif

Motif pattern discovered

Motif recognition program

d

Time (CPU sec.)


hm01

gggaggctgaggcatgag

cggaggcctaagcctcag

GLAM [22]

18

8

42.1

hm03

Cagccaggctgcagtgctg

Catccatacagaa

GLAM [22]

13

6

12.3

hm04

gcgatgtgtaatagtcgc

gacatgtgtaaaaga

MEME [11]

15

9

54.2

hm08

ggagaaattctaa

aTGACgTC

Weeder [14]

13

6

4.34

hm20

ctgTAatc

gagTAaac

MITRA [6]

8

3

6.7

hm26

GCCGGC

GCCGGC

MITRA [6]

6

0

3.44


Data collected from TRANSFAC and the published motifs are found by the assessment of Tompa et. al. [2] of differing motif tools. For each set of data, we determined motifs of the same length using sMCL-WMR. The number of strings ranges from 8 to 34.

Boucher and King BMC Bioinformatics 2010 11(Suppl 1):S11   doi:10.1186/1471-2105-11-S1-S11

Open Data