Protocol
It is important when using this technique to decide which genome your sequence should be aligned to. More divergent species will have less sequence homology between orthologous genes. Therefore, the key is to pick species that are related enough to detect homology, but divergent enough to maximize non-alignment "noise". Step wise approach to Phylogenetic footprinting consists of :
- One should decide on the gene of interest.
- Carefully choose species with orthologous genes.
- Decide on the length of the upstream or maybe downstream region to be looked at.
- Align the sequences.
- Look for conserved regions and analyse them.
Read more about this topic: Phylogenetic Footprinting