Figure 10.

Average TFBS detection accuracy of five alignment tools. The y-axis shows the TFBS detection accuracy average of six TFBSs, and the x-axis is the divergence scale coefficient of the mammalian phylogenetic tree (Figure 9). SimuALN stands for the simulated alignment and its measure indicates the proportion of TFBS nucleotides not subject to replacement turnover in descendent sequences, and thus aligned in simulated alignments. Plots in the left panel show the overall detection accuracy of all functional TFBSs, while those in the right panel show the detection accuracy on the subset of TFBSs that had not turned over. Note that insertion and deletion events may affect parts of a binding site (these are still included in the evaluation), and that SimuALN consequently does not reach a level of one in the right panels. (a) Two species alignments of human and baboon. (b) Three species alignments of human, baboon and mouse. (c) Four species alignments of human, baboon, mouse, and dog. (d) Five species alignment.

Huang et al. Genome Biology 2007 8:R225   doi:10.1186/gb-2007-8-10-r225
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