Accuracy
It is important to keep in mind that not all conserved sequences are under selection pressure. To eliminate false positives statistical analysis must be performed that will show that the motifs reported have a mutation rate meaningfully less than that of the surrounding nonfunctional sequence.
Moreover, results could be more accurate if the prior knowledge about the sequence is considered. For example, some regulatory elements are repeated 15 times in a promoter region (e.g., some metallothionein promoters have up to 15 metal response elements (MREs)). Thus, to eliminate false motifs with inconsistent order across species, the orientation and order of regulatory elements in a promoter region should be the same in all species. This type of information could help us to identify regulatory elements that are not adequately conserved but occur in several copies in the input sequence.
Read more about this topic: Phylogenetic Footprinting
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