Skip to main content

Table 1 Multiple alignment results in orthologous sequences

From: Multiple non-collinear TF-map alignments of promoter regions

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
  1. 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.