Fast motif recognition via application of statistical thresholds

BMC Bioinformatics

Table 4 Motif recognition on biological data.

Data set	Published motif	Motif pattern discovered	Motif recognition program	ℓ	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.

ISSN: 1471-2105