I am working on finding conserved elements in plant promoter regions. To find these, I want to compare orthologous promoter regions. Right now, I simply BLAST my region of interest (e.g. 1000 bp upstream of an Arabidopsis gene) to my other species of interest, and then take the best hits. There are however some problems with this approach: a) i find very short hits, and b) some hits are obviously nonsense (arabidopsis chromosome 1 sequence returns mitochondrial sequence of other species).
One of my potential solutions is using the PLAZA4.0 database to first find the best orthologous gene in the other species (rather than looking for an orthologous promoter), and then retrieve the upstream sequence of that gene.
Please let me know if you think either of my approaches makes sense, or if you have any other ideas.