Multiple non-collinear TF-map alignments of promoter regions

BMC Bioinformatics

Table 1 Multiple alignment results in orthologous sequences

HRCZ SET	MMA		CLUSTALW		MLAGAN		FOOTPRINTER
	TOP1	Avg.Score	TOP1	Avg. score	TOP1	Avg. score	TOP1	Avg. Motifs
Coding	6	17.15	27	3706.72	26	3739.58	23	20.41
5'UTR	2	10.48	4	2671.78	4	2742.92	3	11.66
Promoter	18	25.41	4	2005.67	4	2114.00	5	8.66
3'UTR	7	15.85	1	1994.22	1	2046.31	3	9.63
Intronic	2	8.34	0	1267.89	0	1268.42	1	3.00
Downstream	0	6.85	0	1174.28	1	1245.47	1	2.02
5'Intergenic	0	5.42	0	1052.92	0	1092.28	0	0.75
3'Intergenic	1	4.14	0	974.69	0	1027.58	0	0.44

TF-map and sequence alignments (CLUSTALW [5], MLAGAN [31], FOOTPRINTER [32]) of different genomic regions between the human, mouse, chicken and zebrafish orthologous promoters in the HRCZ SET. TOP1 is the number of genes in which the highest scoring alignment is found in a given genomic region. The MMA results were obtained with the optimal configuration α = 1; λ = 0.3; μ = 0.1; γ = 2.

ISSN: 1471-2105